From sandmann at embl.de Tue May 1 05:39:27 2007 From: sandmann at embl.de (Thomas Sandmann) Date: Tue, 1 May 2007 14:39:27 +0200 Subject: [Genome] Drosophila release 5.1 Message-ID: Dear UCSC team, I was wondering if you are planning to update the Drosophila tracks to the new release (5.1) soon ? Thanks, Thomas From kuhn at soe.ucsc.edu Tue May 1 09:30:28 2007 From: kuhn at soe.ucsc.edu (Robert Kuhn) Date: Tue, 1 May 2007 09:30:28 -0700 Subject: [Genome] blat perl script Message-ID: <200705011630.JAA07771@moondance.cse.ucsc.edu> hello, sung, the block on your IP decays slowly. perhaPs it is still in place from earlier. Send me your IP address directly (not to the list) and I will look into it. --b0b kuhn ucsc genome bioinformatics group > From genome-bounces at soe.ucsc.edu Tue May 1 08:04:19 2007 > To: genome at cse.ucsc.edu > Subject: [Genome] blat perl script > > Hi, > > as was suggested, i am using the blat script available from http://genomewiki.cse.ucsc.edu/index.php/Blat_Scripts. i have 1 large file containing ~1000 sequences i would like to blat. when i submit this perl script, i am still receiving "high traffic error messages". Am I using this script correctly? or should i lengthen the wait time between job submissions? > > > thank you > > cheers > > > sung > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome > From galt at soe.ucsc.edu Tue May 1 10:23:39 2007 From: galt at soe.ucsc.edu (Galt Barber) Date: Tue, 1 May 2007 10:23:39 -0700 (PDT) Subject: [Genome] short mm8 chr1 and 2? In-Reply-To: References: <20070430170258.AOB28137@m4500-01.uchicago.edu> Message-ID: Smart http clients can auto-resume an interrupted download because http 1.1 supports range requests which can ask for any part of the file. wget -c allows you to do this with http to "continue" to download. -Galt On Mon, 30 Apr 2007, Rachel Harte wrote: > Hello Ben, > > It may be that if you are using Windows and http then the files are not > being completely downloaded. Try using wget and ftp instead e.g. for chr1: > wget > 'ftp://hgdownload.cse.ucsc.edu/apache/htdocs/goldenPath/mm8/chromosomes/chr1.fa.gz' > -O chr1.fa.gz > > --18:54:24-- > ftp://hgdownload.cse.ucsc.edu/apache/htdocs/goldenPath/mm8/chromosomes/chr1.fa.gz > => `chr1.fa.gz' > Resolving hgdownload.cse.ucsc.edu... 128.114.119.140 > Connecting to hgdownload.cse.ucsc.edu|128.114.119.140|:21... connected. > Logging in as anonymous ... Logged in! > ==> SYST ... done. ==> PWD ... done. > ==> TYPE I ... done. ==> CWD /apache/htdocs/goldenPath/mm8/chromosomes > ... done. > ==> PASV ... done. ==> RETR chr1.fa.gz ... done. > Length: 62,819,741 (60M) (unauthoritative) > > 100%[====================================>] 62,819,741 13.69M/s ETA > 00:00 > > 18:54:28 (14.16 MB/s) - `chr1.fa.gz' saved [62819741] > > then > >sum chr1.fa.gz > 52962 61348 > > For chr2: > --18:58:03-- > ftp://hgdownload.cse.ucsc.edu/apache/htdocs/goldenPath/mm8/chromosomes/chr2.fa.gz > => `chr2.fa.gz' > Resolving hgdownload.cse.ucsc.edu... 128.114.119.140 > Connecting to hgdownload.cse.ucsc.edu|128.114.119.140|:21... connected. > Logging in as anonymous ... Logged in! > ==> SYST ... done. ==> PWD ... done. > ==> TYPE I ... done. ==> CWD /apache/htdocs/goldenPath/mm8/chromosomes > ... done. > ==> PASV ... done. ==> RETR chr2.fa.gz ... done. > Length: 58,461,619 (56M) (unauthoritative) > > 100%[====================================>] 58,461,619 14.54M/s ETA > 00:00 > > 18:58:07 (14.51 MB/s) - `chr2.fa.gz' saved [58461619] > > then > > sum chr2.fa.gz > 24876 57092 > > If your result does not look like the output above then the file is not > being downloaded completely. > > I hope that this helps you. Please let us know if you have further > questions. > > Rachel > > Rachel Harte > UCSC Genome Bioinformatics Group > http://genome.ucsc.edu > > > On Mon, 30 Apr 2007, Ben Gantner wrote: > > > Hi there: > > > > Sorry for the bother but I've tried repeatedly to download > > the mm8 release of the mouse genome from your site. I'm > > downloading gzipped files from the following page: > > http://hgdownload.cse.ucsc.edu/goldenPath/mm8/chromosomes/ > > > > When I decompress the files I count the total sequence length > > per chromosome (minus headers) and I get back the correct > > lengths for most of the chromosomes as described on your > > site: > > http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=86540626&chromInfoPage= > > > > However, chr1 and chr2 show up short, and I'm missing a > > significant amount of sequence: > > chr1 get : 115212860, expect : 197,069,962 > > chr2 get : 102088474, expect : 181,976,762 > > > > I've looked through the site FAQ and can't find anything > > about this, any suggestions/ideas?? > > > > Thanks so much, > > Ben > > _________________________ > > Ben Gantner > > University of Chicago > > Singh Lab, CIS Rm W519 > > 929 East 57th Street > > Chicago, IL 60637 > > (Ph) 773.702.2912 > > _______________________________________________ > > Genome maillist - Genome at soe.ucsc.edu > > http://www.soe.ucsc.edu/mailman/listinfo/genome > > > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome > From kayla at soe.ucsc.edu Tue May 1 10:31:14 2007 From: kayla at soe.ucsc.edu (Kayla Smith) Date: Tue, 01 May 2007 10:31:14 -0700 Subject: [Genome] Drosophila release 5.1 In-Reply-To: References: Message-ID: <46377962.1060806@cse.ucsc.edu> Thomas, The new Drosophila browser (dm3) is currently in development, but you can take a look at it on our test server: http://genome-test.cse.ucsc.edu However, keep in mind that the data here has not gone through our usual quality assurance procedures and so may have errors. Kayla Smith UCSC Genome Bioinformatics Group Thomas Sandmann wrote: > Dear UCSC team, > > I was wondering if you are planning to update the Drosophila tracks > to the new release (5.1) soon ? > > Thanks, > Thomas > > > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome From kayla at soe.ucsc.edu Tue May 1 11:14:11 2007 From: kayla at soe.ucsc.edu (Kayla Smith) Date: Tue, 01 May 2007 11:14:11 -0700 Subject: [Genome] genes for specific organ In-Reply-To: <131289.75682.qm@web63204.mail.re1.yahoo.com> References: <131289.75682.qm@web63204.mail.re1.yahoo.com> Message-ID: <46378373.1050705@cse.ucsc.edu> Jay an, You can find which genes are expressed in a certain tissue type by using the table browser. Here are two previously answered mailinglist questions with instructions on how to get this information in two different ways: http://www.soe.ucsc.edu/pipermail/genome/2006-September/011685.html http://www.soe.ucsc.edu/pipermail/genome/2006-April/010327.html I hope this information is helpful to you. Please don't hesitate to contact us again if you require further assistance. Kayla Smith UCSC Genome Bioinformatics Group Jay an wrote: > hello, > > can you tell me how I can get genes labeled by different organs? > > such as: gene1, gene2,......==> liver > gene1, gene5,.... ==> kidney > > > > --------------------------------- > Ahhh...imagining that irresistible "new car" smell? > Check outnew cars at Yahoo! Autos. > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome From donlinmj at slu.edu Tue May 1 09:16:47 2007 From: donlinmj at slu.edu (Maureen J Donlin) Date: Tue, 01 May 2007 11:16:47 -0500 Subject: [Genome] Using tables to batch extract sequence data Message-ID: <7.0.1.0.2.20070501110623.00ed02c0@slu.edu> Hi, I am trying to use the Tables feature to batch extract sequence from the mouse genome. I set the following tracts: genome: Mouse assembly: Feb 2006 group: Mapping and Sequencing tracts track: Assembly I used the defined regions and input the following: chr8:86583389-86583638 chr8:24602164-24602613 chr7:126691122-126691571 Output format: sequence Click on get output Do not add any extra bases When I click on get sequence, I get back >mm8_gold_AC164432.3 range=chr8:86537462-86658633 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none which is over 100 Kb of sequence rather than just the region I put in. What am I doing wrong? When I put in chr8:86583389-86583638 in the position/search box of the browser and click the DNA button at the top, I get back just that region. Any suggestions would be appreciated as I have ~200 regions to pull out. thanks, Maureen Donlin Maureen J. Donlin, Ph.D. Assistant Research Professor Dept. of Biochemistry & Molecular Biology Saint Louis University School of Medicine 1402 S Grand M411 Schwitalla Hall St. Louis, MO 63104 314-977-8858 From kayla at soe.ucsc.edu Tue May 1 11:34:02 2007 From: kayla at soe.ucsc.edu (Kayla Smith) Date: Tue, 01 May 2007 11:34:02 -0700 Subject: [Genome] Using tables to batch extract sequence data In-Reply-To: <7.0.1.0.2.20070501110623.00ed02c0@slu.edu> References: <7.0.1.0.2.20070501110623.00ed02c0@slu.edu> Message-ID: <4637881A.8090106@cse.ucsc.edu> Maureen, What's happening is that you're getting all the assembly fragments which contain your user defined regions. The way to get just the sequence data you want is to first make a Custom Track and then use the table browser to get sequence from that Custom Track. Here is a link to where you can paste in your custom track: http://genome.ucsc.edu/cgi-bin/hgCustom Keep in mind that when you're pasting your regions into the Custom Track tool, that they need to be in BED format (i.e. take out the colons and the dashes) chr8 86583389 86583638 chr8 24602164 24602613 chr7 126691122 126691571 Back in the Table Browser, toggle the "group" pulldown menu to "Custom Tracks", track: "User Track", and table: "ct_UserTrack" (or whatever you named your custom track). Set region: "genome", and output format: "sequence". I hope this helps you to get the data you are looking for. Please don't hesitate to contact us again if you require further assistance. Kayla Smith UCSC Genome Bioinformatics Group Maureen J Donlin wrote: > Hi, > > I am trying to use the Tables feature to batch extract sequence from > the mouse genome. I set the following tracts: > genome: Mouse > assembly: Feb 2006 > group: Mapping and Sequencing tracts > track: Assembly > > I used the defined regions and input the following: > chr8:86583389-86583638 > chr8:24602164-24602613 > chr7:126691122-126691571 > > Output format: sequence > Click on get output > Do not add any extra bases > > When I click on get sequence, I get back > >mm8_gold_AC164432.3 range=chr8:86537462-86658633 5'pad=0 3'pad=0 > revComp=TRUE strand=- repeatMasking=none > which is over 100 Kb of sequence rather than just the region I put in. > What am I doing wrong? When I put in chr8:86583389-86583638 in the > position/search box of the browser and click the DNA button at the > top, I get back just that region. > > Any suggestions would be appreciated as I have ~200 regions to pull out. > > thanks, > Maureen Donlin > > > > > Maureen J. Donlin, Ph.D. > > Assistant Research Professor > Dept. of Biochemistry & Molecular Biology > Saint Louis University School of Medicine > > 1402 S Grand > M411 Schwitalla Hall > St. Louis, MO 63104 > 314-977-8858 > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome From zxu at uhnres.utoronto.ca Tue May 1 13:49:31 2007 From: zxu at uhnres.utoronto.ca (Zhaodong Xu) Date: Tue, 01 May 2007 16:49:31 -0400 Subject: [Genome] [Fwd: extracting human genes from mouse expression arrays] Message-ID: <4637A7DB.4A5CAEE7@uhnres.utoronto.ca> hi, my collegue want to extract the accession data from the mouse data and convert them to human accession numbers, what kind of Table should I query to? thanks zhaodong -------- Original Message -------- Subject: extracting human genes from mouse expression arrays Date: Mon, 30 Apr 2007 16:21:26 -0400 From: izhar livnebar To: zxu at uhnres.utoronto.ca Hello Zhadong, Rod wants me to generate heat maps from the expression array of retinoblastoma samples. the heat maps should be of functional groups that are active in the retina (Cell cycle, RNA metabolism etc.). Can you find a way to extract the accession data for these groups from the mouse papers below and convert them to human accession numbers so I can import it into the my array analysis ? thanks, Izzy Samuel Shao-Min Zhang,1,5 Xuming Xu,1 Mu-Gen Liu,1 Hongyu Zhao,2 Marcelo Bento Soares,3 Colin J Barnstable,1,5 and Xin-Yuan Fu4 BMC Dev Biol. 2006; 6: 48. A biphasic pattern of gene expression during mouse retina development Blackshaw S, Fraioli RE, Furukawa T, Cepko CL. Comprehensive analysis of photoreceptor gene expression and the identification of candidate retinal disease genes. Cell. 2001;107:579?589. doi: 10.1016/S0092-8674(01)00574-8. [PubMed] Blackshaw S, Harpavat S, Trimarchi J, Cai L, Huang H, Kuo WP, Weber G, Lee K, Fraioli RE, Cho SH, et al. Genomic analysis of mouse retinal development. PLoS Biol. 2004;2:E247. doi: 10.1371/journal.pbio.0020247. [PubMed] Zhaodong Xu , Zuyao From kayla at soe.ucsc.edu Tue May 1 15:58:58 2007 From: kayla at soe.ucsc.edu (Kayla Smith) Date: Tue, 01 May 2007 15:58:58 -0700 Subject: [Genome] [Fwd: extracting human genes from mouse expression arrays] In-Reply-To: <4637A7DB.4A5CAEE7@uhnres.utoronto.ca> References: <4637A7DB.4A5CAEE7@uhnres.utoronto.ca> Message-ID: <4637C632.6010309@cse.ucsc.edu> Zhaodong, The hg18.mmBlastTab (and mm8.hgBlastTab) tables will be of interest to you. They connect human UCSC ids with mouse accession names. Please see this previously answered mailinglist question which asks a similar question to yours: https://www.soe.ucsc.edu/pipermail/genome/2007-March/013096.html Also since your college mentions expression data in the email you attached below, I want to point out a useful resource available that is available. We display some expression data in both our human and mouse browsers which you may be interested in. When in the Genome Browser, scroll down to the "Expression and Regulation" track controls. The GNF Atlas 2 tracks are popular. I hope this information is helpful to you. Please don't hesitate to contact us again if you require further assistance. Kayla Smith UCSC Genome Bioinformatics Group Zhaodong Xu wrote: > hi, > > my collegue want to extract the accession data from the mouse data and > convert them to human accession numbers, what kind of Table should I > query to? > > thanks > > > zhaodong > > -------- Original Message -------- > Subject: extracting human genes from mouse expression arrays > Date: Mon, 30 Apr 2007 16:21:26 -0400 > From: izhar livnebar > To: zxu at uhnres.utoronto.ca > > Hello Zhadong, Rod wants me to generate heat maps from the expression > array of retinoblastoma samples. the heat maps should be of functional > groups that are active in the retina (Cell cycle, RNA metabolism > etc.). Can you find a way to extract the accession data for these > groups from the mouse papers below and convert them to human accession > numbers so I can import it into the my array analysis ? > thanks, Izzy > > Samuel Shao-Min Zhang,1,5 Xuming Xu,1 Mu-Gen Liu,1 Hongyu Zhao,2 > Marcelo Bento Soares,3 Colin J Barnstable,1,5 and Xin-Yuan Fu4 > BMC Dev Biol. 2006; 6: 48. > A biphasic pattern of gene expression during mouse retina development > > Blackshaw S, Fraioli RE, Furukawa T, Cepko CL. Comprehensive analysis > of photoreceptor gene expression and the identification of candidate > retinal disease genes. Cell. 2001;107:579?589. doi: > 10.1016/S0092-8674(01)00574-8. [PubMed] > > Blackshaw S, Harpavat S, Trimarchi J, Cai L, Huang H, Kuo WP, Weber G, > Lee K, Fraioli RE, Cho SH, et al. Genomic analysis of mouse retinal > development. PLoS Biol. 2004;2:E247. doi: > 10.1371/journal.pbio.0020247. [PubMed] > Zhaodong Xu , Zuyao > > > ------------------------------------------------------------------------ > > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome From ohs at pl.jaring.my Wed May 2 00:04:47 2007 From: ohs at pl.jaring.my (Hong Sain, Ooi) Date: Wed, 02 May 2007 15:04:47 +0800 Subject: [Genome] The CR596993 record in all_mrna table Message-ID: <4638380F.50002@pl.jaring.my> Dear all, I have a question regarding the CR596993 record in all_mrna table. It was an entry in the table before (up to March 2007) but was deleted from the latest version. The following is the link to the record in NCBI Genbank, http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=50477800 The record is marked as HTC (unfinished high-throughput cDNA sequencing) which may suggest the incompleteness of the mRNA sequence. My question is, why the record was included in the all_mrna table previously and subsequently was removed. What are the criteria used to remove it? Have a nice day. Best regards, Hong Sain, Ooi From akarger at CGR.Harvard.edu Wed May 2 08:20:05 2007 From: akarger at CGR.Harvard.edu (Amir Karger) Date: Wed, 2 May 2007 11:20:05 -0400 Subject: [Genome] isPcr doesn't find an amplicon? Message-ID: Hi. I put the following primer pair into isPcr (command line and web version), and got no results. I've confirmed that I can get results with other primers, so I know I'm using it correctly. ENSG00000000457_E13A_P14 TTCCACCTCCGCGTGC AGCTTTAGGACCCTC isPcr should be finding chr20:59,627,734-59,627,760 on the + strand. I've confirmed with the Genome Browser that the forward primer and the complement of the reverse primer do appear at those positions on chr20. Could you tell me why isPcr isn't finding it? I thought maybe one of the primers was a repeat, but at least my command-line version isn't doing any masking: I just did isPcr chr20.fa primers.tab primers.fasta. Thanks, - Amir Karger Research Computing Life Sciences Division Harvard University 617-496-0626 From ann at soe.ucsc.edu Wed May 2 09:42:25 2007 From: ann at soe.ucsc.edu (Ann Zweig) Date: Wed, 02 May 2007 09:42:25 -0700 Subject: [Genome] The CR596993 record in all_mrna table In-Reply-To: <4638380F.50002@pl.jaring.my> References: <4638380F.50002@pl.jaring.my> Message-ID: <4638BF71.1050805@cse.ucsc.edu> Hello Hong Sain, Ooi- In mid-April we changed the filters that we use when we query the GenBank database. The change included rejecting all entries which contain: "http://fulllength.invitrogen.com". Some of these entries have been aligned to pseudogenes and modified to match the genome, making it appear as if the genes are transcribed. Invitrogen no longer sells the clones, and the URL is a broken link. Regards, ---------- Ann Zweig UCSC Genome Bioinformatics Group http://genome.ucsc.edu We invite you to give us your feedback on the UCSC Genome Browser through May 31, 2007: http://www.surveymonkey.com/s.asp?U=881163743177 Hong Sain, Ooi wrote: > Dear all, > > I have a question regarding the CR596993 record in all_mrna table. It > was an entry in the table before (up to March 2007) but was deleted from > the latest version. The following is the link to the record in NCBI Genbank, > http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=50477800 > > The record is marked as HTC (unfinished high-throughput cDNA sequencing) > which may suggest the incompleteness of the mRNA sequence. My question > is, why the record was included in the all_mrna table previously and > subsequently was removed. What are the criteria used to remove it? > > Have a nice day. > > Best regards, > Hong Sain, Ooi > > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome From ueli.gubler at roche.com Wed May 2 10:00:31 2007 From: ueli.gubler at roche.com (Gubler, Ueli) Date: Wed, 2 May 2007 13:00:31 -0400 Subject: [Genome] (no subject) Message-ID: To whom it may concern: Is the data as published in Cell 128, 1231, March 2007, Kim et al (from the Ludwig Institute, Bing Ren lab), on CTCF-binding sites already accessible thru the UCSC genome browser? Thank you for your help in this matter. Sincerely, Ueli Gubler From ann at soe.ucsc.edu Wed May 2 10:37:45 2007 From: ann at soe.ucsc.edu (Ann Zweig) Date: Wed, 02 May 2007 10:37:45 -0700 Subject: [Genome] isPcr doesn't find an amplicon? In-Reply-To: References: Message-ID: <4638CC69.7030506@cse.ucsc.edu> Hello Amir, When I search for ENSG00000000457 in the Genome Browser, I find two transcripts located at: chr1:168,088,839-168,129,717. Likewise, when I look it up on the Ensembl website, they place it at the same location on chr1. Are you working on the latest human assembly: hg18? Please give us more details, and we can help clear things up for you. Regards, ---------- Ann Zweig UCSC Genome Bioinformatics Group http://genome.ucsc.edu We invite you to give us your feedback on the UCSC Genome Browser through May 31, 2007: http://www.surveymonkey.com/s.asp?U=881163743177 Amir Karger wrote: > Hi. > > I put the following primer pair into isPcr (command line and web > version), and got no results. I've confirmed that I can get results with > other primers, so I know I'm using it correctly. > > ENSG00000000457_E13A_P14 TTCCACCTCCGCGTGC AGCTTTAGGACCCTC > > isPcr should be finding chr20:59,627,734-59,627,760 on the + strand. > > I've confirmed with the Genome Browser that the forward primer and the > complement of the reverse primer do appear at those positions on chr20. > > Could you tell me why isPcr isn't finding it? I thought maybe one of the > primers was a repeat, but at least my command-line version isn't doing > any masking: I just did isPcr chr20.fa primers.tab primers.fasta. > > Thanks, > - Amir Karger > Research Computing > Life Sciences Division > Harvard University > 617-496-0626 > > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome From ann at soe.ucsc.edu Wed May 2 11:35:06 2007 From: ann at soe.ucsc.edu (Ann Zweig) Date: Wed, 02 May 2007 11:35:06 -0700 Subject: [Genome] (no subject) In-Reply-To: References: Message-ID: <4638D9DA.1070602@cse.ucsc.edu> Hello Ueli, We certainly host several data sets from the Bing Ren lab, however, it is unclear if we are hosting the set referred to in this paper. If we do have these data, you would likely find the track in the hg17 assembly, in the ENCODE Chromatin Immunoprecipitation section. I would suggest contacting either of the corresponding authors for the exact name of the track: Tae Hoon Kim taehoon.kim at yale.edu Bing Ren biren at ucsd.edu Sorry I can't be of more help. Regards, ---------- Ann Zweig UCSC Genome Bioinformatics Group http://genome.ucsc.edu We invite you to give us your feedback on the UCSC Genome Browser through May 31, 2007: http://www.surveymonkey.com/s.asp?U=881163743177 Gubler, Ueli wrote: > To whom it may concern: > > Is the data as published in Cell 128, 1231, March 2007, Kim et al (from > the Ludwig Institute, Bing Ren lab), on CTCF-binding sites already > accessible thru the UCSC genome browser? > > Thank you for your help in this matter. > > Sincerely, > > Ueli Gubler > > > > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome From ajones at cshl.edu Wed May 2 12:37:48 2007 From: ajones at cshl.edu (Jones, Adrienne) Date: Wed, 02 May 2007 15:37:48 -0400 Subject: [Genome] ExonPrimer Tool Message-ID: Hi, I have a question about the output from exonprimer. What do the uppercase versus lowercase nucleotides mean? Also what do the X's *'s and .'s signify? Thanks for your help. From ann at soe.ucsc.edu Wed May 2 14:25:59 2007 From: ann at soe.ucsc.edu (Ann Zweig) Date: Wed, 02 May 2007 14:25:59 -0700 Subject: [Genome] [no subject] In-Reply-To: References: Message-ID: <463901E7.4090404@cse.ucsc.edu> Hello Rachel, First let's make sure we are looking at the same position. The human alpha-globin gene cluster is located on chromosome 16 at about: chr16:155,973-167,530. Is this the area you are interested in? Now, I will address your questions one-by-one. First. I see a short span in the Conservation track where the mouse line is blank, but I do not see such a span in the rat. The blank area in the mouse is at approximately chr16:159,527-160,355. In this case, there just isn't any sequence in the mouse that aligns to the human sequence in that location. Second. Use the Table Browser to download the aligning sequence (press Tables in the blue navigation bar). Configure it like so: genome: Human assembly: Mar 2006 group: Comparative Genomics track: Conservation table: multiz17way region: (choose the region in which you are interested) output format: MAF To read more about the MAF file format see this FAQ: http://genome.ucsc.edu/FAQ/FAQformat#format5 Third. No. However, we do have a TFBS track. Turn on the track named: TFBS Conserved. This track contains the location and score of transcription factor binding sites conserved in the human/mouse/rat alignment. I hope this is helpful to you. Regards, ---------- Ann Zweig UCSC Genome Bioinformatics Group http://genome.ucsc.edu We invite you to give us your feedback on the UCSC Genome Browser through May 31, 2007: http://www.surveymonkey.com/s.asp?U=881163743177 > Subject: > From: > Rachel.J.West at Dartmouth.EDU (Rachel J. West) > Date: > 02 May 2007 15:04:01 -0400 > To: > genome at soe.ucsc.edu > > > Hi there- > > I have just begun using your Genome Browser, and although I have found > it helpful, I have some questions. > > First- I am examining a noncoding region around the alpha-globin > cluster, looking for regions of conservation between humans and other > vertebrates. In the alignment display, there are dots, dashes, and > double-dashes- all of which I understand. But what does a 'blank' mean? > For instance, mouse and rat are both blank this region, though I believe > their genomes are fully sequences; is the area siimply too divergent? > > Second-I would like to download the sequence in this region for each of > the organisms for which there is some similarity; how do I do that? > > Third- is there a search engine embedded in your program that will > search for potential transcription-factor-binding sites, and tell me > what they are? > > Thank you! I'll look forward to your response. > > R From ann at soe.ucsc.edu Wed May 2 14:34:25 2007 From: ann at soe.ucsc.edu (Ann Zweig) Date: Wed, 02 May 2007 14:34:25 -0700 Subject: [Genome] ExonPrimer Tool In-Reply-To: References: Message-ID: <463903E1.9080300@cse.ucsc.edu> Hello Adrienne, Although we provide a link to the Exon Primer tool, it is not our software. It is run by a group in Germany: Institute of Human Genetics. I would suggest that you contact them and ask them about the output. Probably the best person to contact would be Tim Strom: TimStrom at gsf.de Regards, ---------- Ann Zweig UCSC Genome Bioinformatics Group http://genome.ucsc.edu We invite you to give us your feedback on the UCSC Genome Browser through May 31, 2007: http://www.surveymonkey.com/s.asp?U=881163743177 Jones, Adrienne wrote: > Hi, > > I have a question about the output from exonprimer. What do the uppercase > versus lowercase nucleotides mean? Also what do the X's *'s and .'s signify? > > Thanks for your help. > > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome From cohenjon at mail.nih.gov Wed May 2 21:01:23 2007 From: cohenjon at mail.nih.gov (Cohen, Jonathan (NIH/NICHD) [F]) Date: Thu, 3 May 2007 00:01:23 -0400 Subject: [Genome] REFSEQ and table searching Message-ID: <42504F69898FE546B3F0238C9BD032750DAFE7@NIHCESMLBX7.nih.gov> I am currently using the UCSC genome browser to obtain 3'UTR and 1.5 kb downstream seuqences for human, mouse, rat to perform motif anaylsis on sets of differentially regulated genes. IN doing this, I have had to convert unigene symbols and/or accession numbers into reference sequence accessions using DAVID (http://david.abcc.ncifcrf.gov/) . However, when I submit the REFSEQ to UCSC, I dont not get back a matching list of genes. Wouldnt the fact that these are REFSEQs mean that they have their 3'UTR in the database? Here are 2 examples: Gene name Trim44 Cluster Rn.8005 LLID 362172 GENE NAME TRIPARTITE MOTIF-CONTAINING 44 REFSEQ NM_001013203 SPECIES 10116:RATTUS NORVEGICUS When I try to retrive 3'UTR and 1.5 kb using the table browser, nothing comes back. If I BLAT it, there is a REFSEQ entry which I can click on to retrieve 3' sequence. Antoher example is Gene name Tarbp2 Cluster Rn.17227 LLID 363006 GENE NAME TAR (HIV) RNA BINDING PROTEIN 2 REFSEQ NM_001034941 SPECIES 10116:RATTUS NORVEGICUS Has anyone had this problem? From imke.puls at charite.de Wed May 2 21:53:55 2007 From: imke.puls at charite.de (Imke Puls) Date: Thu, 3 May 2007 06:53:55 +0200 (CEST) Subject: [Genome] polymorphic markers Message-ID: <1139.141.42.65.201.1178168035.squirrel@webmail.charite.de> Hello, We are searching for di-, tri-, and tetranucleotide marker in specific genomic regions. The section STS marker of the Human genome Browser did not give any marker within these regions. Are they always named DS...? Do you have any other information where we could look for these sequences? Thanks a lot for your help, Imke Puls Prof. Dr. I. Puls Leiterin AG Genetik Klinik f?r Psychiatrie und Psychotherapie Charit? Campus Mitte - Universit?tsmedizin Charit?platz 1 D-10117 Berlin Tel: 030-450-617357 oder 450-517357 (AB) Fax: 030-450-517953 Email: imke.puls at charite.de From klaus.stark at klinik.uni-regensburg.de Thu May 3 01:52:13 2007 From: klaus.stark at klinik.uni-regensburg.de (Klaus Stark) Date: Thu, 03 May 2007 10:52:13 +0200 Subject: [Genome] problems with export to ps Message-ID: <4639BEDD.2081.409534@klaus.stark.klinik.uni-regensburg.de> Hallo together! You are really doing a good job! But since a few days the export to ps does not function properly. It is always cut on the right side. The phenonemon is independent of the browser used. I hope you can fixed it or help me to solve it locally. Thanks in advance. Best regards, Klaus -- Dr. rer. nat. Klaus Stark Klinik und Poliklinik f?r Innere Medizin II Kardiologie - Forschung Universit?tsklinikum Regensburg Forschungsbau H1 Raum 13 Franz-Josef-Strauss-Allee 11 93053 Regensburg Tel.: +49-941-944-7340 Fax: +49-941-944-7341 From hartera at soe.ucsc.edu Thu May 3 09:17:49 2007 From: hartera at soe.ucsc.edu (Rachel Harte) Date: Thu, 3 May 2007 09:17:49 -0700 (PDT) Subject: [Genome] polymorphic markers In-Reply-To: <1139.141.42.65.201.1178168035.squirrel@webmail.charite.de> References: <1139.141.42.65.201.1178168035.squirrel@webmail.charite.de> Message-ID: Hello Imke Puls, You could try looking in the Microsatellite track. The track control to switch this track on is in the "Variation and Repeats" group under the Genome Browser image. If you know the sequences that you are you searching for, then you could use the Short Match track (in the Mapping and Sequencing Tracks group). If you click on the "Short Match" link above the track control for the track, then you can type a sequence of 2-30 bases into the text box and these will be marked in the track across the genome. I did not see many markers in human whose name begins with "DS" but there are several hundred that begin with "D8S". These may be all from the same source. Not all the markers have names with this prefix. I hope that this helps you. Please let us know if you have further questions. Rachel Rachel Harte UCSC Genome Bioinformatics Group http://genome.ucsc.edu On Thu, 3 May 2007, Imke Puls wrote: > Hello, > We are searching for di-, tri-, and tetranucleotide marker in specific > genomic regions. The section STS marker of the Human genome Browser did not > give any marker within these regions. Are they always named DS...? Do you > have any other information where we could look for these sequences? > Thanks a lot for your help, Imke Puls > > > > Prof. Dr. I. Puls > Leiterin AG Genetik > Klinik f?r Psychiatrie und Psychotherapie > Charit? Campus Mitte - Universit?tsmedizin > Charit?platz 1 > D-10117 Berlin > Tel: 030-450-617357 oder 450-517357 (AB) > Fax: 030-450-517953 > Email: imke.puls at charite.de > > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome > From hartera at soe.ucsc.edu Thu May 3 09:23:50 2007 From: hartera at soe.ucsc.edu (Rachel Harte) Date: Thu, 3 May 2007 09:23:50 -0700 (PDT) Subject: [Genome] problems with export to ps In-Reply-To: <4639BEDD.2081.409534@klaus.stark.klinik.uni-regensburg.de> References: <4639BEDD.2081.409534@klaus.stark.klinik.uni-regensburg.de> Message-ID: Hello Klaus, This works ok for me using Mozilla on Linux. However, it may be a platform-dependent, browser-dependent problem. Please send us more details - which operating system are you using (Windows, Linux) and which version? Are you using a PC or a Mac or other machine? Which web browser are you using and what version? With this information, it will be easier for us to figure out what is causing the problem? Thank you. Rachel Rachel Harte UCSC Genome Bioinformatics Group http://genome.ucsc.edu On Thu, 3 May 2007, Klaus Stark wrote: > Hallo together! > > You are really doing a good job! > But since a few days the export to ps does not function properly. It is > always cut on the right side. The phenonemon is independent of the > browser used. > > I hope you can fixed it or help me to solve it locally. > > Thanks in advance. > > Best regards, > Klaus > > -- > Dr. rer. nat. Klaus Stark > Klinik und Poliklinik f?r Innere Medizin II > Kardiologie - Forschung > Universit?tsklinikum Regensburg > Forschungsbau H1 Raum 13 > Franz-Josef-Strauss-Allee 11 > 93053 Regensburg > Tel.: +49-941-944-7340 > Fax: +49-941-944-7341 > > > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome > From ajb97b at leicester.ac.uk Thu May 3 09:36:45 2007 From: ajb97b at leicester.ac.uk (Anthony J Brookes) Date: Thu, 3 May 2007 17:36:45 +0100 (BST) Subject: [Genome] [HGV200X] HGV2007: FEW DAYS TO APPLICATION DEADLINE (15th May 2007) Message-ID: 9th International Meeting On HUMAN GENOME VARIATION AND COMPLEX GENOME ANALYSIS Dear Colleague, The application deadline for the above meeting ('HGV2007') is now only a FEW DAYS AWAY (15th May 2007). The meeting itself will be held from 6th (midday) - 8th (evening) September 2007 at the Hotel Dolce Sitges Conference Center, near Barcelona, Spain. This is a 5-star venue in a region of exceptional natural beauty. A registration form, plus further details of the meeting, can be found at http://hgv2007.nci.nih.gov/ A flyer for the meeting can be downloaded from http://hgv2007.nci.nih.gov/HGV2007_Flyer_2.pdf The symposium will focus upon the latest breakthroughs and challenges concerned with genome variation, particularly aspects such as methods/strategies for effective utilization of SNPs and CNVs, functional genomics applications, bioinformatics, population genetics, ethics, and the study of human disease. Confirmed Speakers: John Armour, Ewan Birney, Esteban Burchard, Anne Cambon-Thomsen, Angel Cariacedo, Vivian Cheung, George Church, Don Conrad, Emmanouil Dermitzakis, Ivo Gut, Matthew Hurles, Iuliana Ionita, Heikki Lehvaslaiho, Debbie Nickerson, Jim Ostell, Chris Ponting, Lincoln Stein, Gilles Thomas, Barbara Trask, Joris Veltman Meeting Format: All sessions will be in plenum with 20-25 minute presentations by invited speakers and others selected from abstracts, with ample time for discussions. All applicants must submit an abstract. Delegates not giving an oral presentation are required to present a poster. Attendance: The number of delegates at HGV2007 will be limited to 150. Applications to attend must include a relevant scientific abstract that will be competitively assessed and used as the basis for acceptance/rejection decisions. Accepted abstracts must be presented in poster or oral format, as allocated. To encourage attendance by students, postdoctoral fellows, and junior faculty member in under-represented groups, a number of meeting grants are available upon request to help defray costs for such individuals. Applications: must be submitted via the meeting website by 15th May 2007. On behalf of the HGV207 Organizers: Anthony Brookes, Stephen Chanock, Nancy Cox, Xavier Estivill, Pui-Yan Kwok, Steve Scherer _______________________________________________ HGV200x mailing list HGV200x at lists.le.ac.uk http://lists.le.ac.uk/mailman/listinfo/hgv200x From chatterb at mail.nih.gov Thu May 3 09:46:30 2007 From: chatterb at mail.nih.gov (Bishwanath Chatterjee) Date: Thu, 03 May 2007 12:46:30 -0400 Subject: [Genome] Question regarding EST panel Message-ID: HI I am looking into EST data for gene RECK chr4:43,896,700-43,965,620 and find some of the EST shows double line after single line and also mRNA panels have different color. I will appreciate if you let me know how to read the double lines or color displays and what it exactly mean? Bishwanath Bishwanath Chatterjee, Ph. D. Building 10 Room 6N240 Laboratory of Developmental Biology National Heart Lung and Blood Institute National Institute of Health Bethesda, MD 20892 Tel 301-451-1672 Fax 301-480-1808 From hartera at soe.ucsc.edu Thu May 3 10:23:48 2007 From: hartera at soe.ucsc.edu (Rachel Harte) Date: Thu, 3 May 2007 10:23:48 -0700 (PDT) Subject: [Genome] Question regarding EST panel In-Reply-To: References: Message-ID: Hello Bishwanath, If you click on the blue/gray button at the left side of the EST track, then you will see some track configuration options at the top of the description page. In the Alignment Gap/Insertion Display Options section, you will see that, by default, "Draw double horizontal lines when both genome and query have an insertion" is checked. So this explains the meaning of the double lines in some EST alignments. You can also see the actual alignment by clicking on the EST alignment in the track and then selecting the alignment link in the EST/Genomic alignments section. I hope that this helps you. Please let us know if you have further questions. Rachel Rachel Harte UCSC Genome Bioinformatics Group http://genome.ucsc.edu On Thu, 3 May 2007, Bishwanath Chatterjee wrote: > HI > I am looking into EST data for gene RECK chr4:43,896,700-43,965,620 and > find some of the EST shows double line after single line and also mRNA > panels have different color. I will appreciate if you let me know how to > read the double lines or color displays and what it exactly mean? > Bishwanath > > Bishwanath Chatterjee, Ph. D. > Building 10 Room 6N240 > Laboratory of Developmental Biology > National Heart Lung and Blood Institute > National Institute of Health > Bethesda, MD 20892 > Tel 301-451-1672 > Fax 301-480-1808 > > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome > From klaus.stark at klinik.uni-regensburg.de Thu May 3 09:31:16 2007 From: klaus.stark at klinik.uni-regensburg.de (Klaus Stark) Date: Thu, 03 May 2007 18:31:16 +0200 Subject: [Genome] problems with export to ps In-Reply-To: References: <4639BEDD.2081.409534@klaus.stark.klinik.uni-regensburg.de> Message-ID: <463A2A75.26946.1E4DDCB@klaus.stark.klinik.uni-regensburg.de> Hi Rachel, Thank you for your answer. I am using MS Windows XP Pro SP2 and Internet Explorer 6.0.2900.2180 as well as Firefox 2.0.0.3 on a PC with AMD CPU. On this machine it worked very well (last download of ps files in February). Best regards, Klaus Datum: Thu, 3 May 2007 09:23:50 -0700 (PDT) Von: Rachel Harte An: Klaus Stark Kopie an: genome at soe.ucsc.edu Betreff: Re: [Genome] problems with export to ps > Hello Klaus, > > This works ok for me using Mozilla on Linux. However, it may be a > platform-dependent, browser-dependent problem. Please send us more > details - which operating system are you using (Windows, Linux) and which > version? Are you using a PC or a Mac or other machine? Which web browser are > you using and what version? > > With this information, it will be easier for us to figure out what is > causing the problem? > > Thank you. > > Rachel > > Rachel Harte > UCSC Genome Bioinformatics Group > http://genome.ucsc.edu > > > On Thu, 3 May 2007, Klaus Stark wrote: > > > Hallo together! > > > > You are really doing a good job! > > But since a few days the export to ps does not function properly. It is > > always cut on the right side. The phenonemon is independent of the > > browser used. > > > > I hope you can fixed it or help me to solve it locally. > > > > Thanks in advance. > > > > Best regards, > > Klaus > > > > -- > > Dr. rer. nat. Klaus Stark > > Klinik und Poliklinik f?r Innere Medizin II > > Kardiologie - Forschung > > Universit?tsklinikum Regensburg > > Forschungsbau H1 Raum 13 > > Franz-Josef-Strauss-Allee 11 > > 93053 Regensburg > > Tel.: +49-941-944-7340 > > Fax: +49-941-944-7341 > > > > > > _______________________________________________ > > Genome maillist - Genome at soe.ucsc.edu > > http://www.soe.ucsc.edu/mailman/listinfo/genome > > -- Dr. rer. nat. Klaus Stark Klinik und Poliklinik f?r Innere Medizin II Kardiologie - Forschung Universit?tsklinikum Regensburg Forschungsbau H1 Raum 13 Franz-Josef-Strauss-Allee 11 93053 Regensburg Tel.: +49-941-944-7340 Fax: +49-941-944-7341 From archanat at soe.ucsc.edu Thu May 3 11:10:31 2007 From: archanat at soe.ucsc.edu (Archana Thakkapallayil) Date: Thu, 03 May 2007 11:10:31 -0700 Subject: [Genome] REFSEQ and table searching In-Reply-To: <42504F69898FE546B3F0238C9BD032750DAFE7@NIHCESMLBX7.nih.gov> References: <42504F69898FE546B3F0238C9BD032750DAFE7@NIHCESMLBX7.nih.gov> Message-ID: <463A2597.1080604@soe.ucsc.edu> Hello Jonathan, I tried these two examples, refSeq: NM_001013203,NM_001034941 for the Rat (rn4) assembly and was able to reteive the 3'UTR and 1.5 kb downstream sequences. I am not sure which table you are looking at. The table that gives this information is called "refGene" under the "group: Genes and Gene Prediction Tracks", "track: RefSeq Genes". You can then paste or upload your list of refSeq identifiers by clicking on the paste/upload list button. Make sure that you select the "genome" radio button. Also, the "refLink" and "kgXref" table (found in the table list associated with the RefSeq Genes and Known Gene track) provides a good cross-reference among the gene identifiers. I hope this information is helpful to you. Please let us know if you have further questions. Regards, Archana UCSC Genome Bioinformatics Group We invite you to give us your feedback on the UCSC Genome Browser through May 31, 2007: http://www.surveymonkey.com/s.asp?U=881163743177 Cohen, Jonathan (NIH/NICHD) [F] wrote: > I am currently using the UCSC genome browser to obtain 3'UTR and 1.5 kb downstream seuqences for human, mouse, rat to perform motif anaylsis on sets of differentially regulated genes. IN doing this, I have had to convert unigene symbols and/or accession numbers into reference sequence accessions using DAVID (http://david.abcc.ncifcrf.gov/) . However, when I submit the REFSEQ to UCSC, I dont not get back a matching list of genes. Wouldnt the fact that these are REFSEQs mean that they have their 3'UTR in the database? Here are 2 examples: > > Gene name Trim44 > Cluster Rn.8005 > LLID 362172 > GENE NAME TRIPARTITE MOTIF-CONTAINING 44 > REFSEQ NM_001013203 > SPECIES 10116:RATTUS NORVEGICUS > > When I try to retrive 3'UTR and 1.5 kb using the table browser, nothing > comes back. If I BLAT it, there is a REFSEQ entry which I can click on > to retrieve 3' sequence. Antoher example is > > Gene name Tarbp2 > Cluster Rn.17227 > LLID 363006 > GENE NAME TAR (HIV) RNA BINDING PROTEIN 2 > REFSEQ NM_001034941 > SPECIES 10116:RATTUS NORVEGICUS > > Has anyone had this problem? > > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome > From hartera at soe.ucsc.edu Thu May 3 11:20:58 2007 From: hartera at soe.ucsc.edu (Rachel Harte) Date: Thu, 3 May 2007 11:20:58 -0700 (PDT) Subject: [Genome] problems with export to ps In-Reply-To: <463A2A75.26946.1E4DDCB@klaus.stark.klinik.uni-regensburg.de> References: <4639BEDD.2081.409534@klaus.stark.klinik.uni-regensburg.de> <463A2A75.26946.1E4DDCB@klaus.stark.klinik.uni-regensburg.de> Message-ID: Klaus, Please would you send the hgsid (in the URL) when you are getting this problem. Also, do you have the next/previous navigation arrows switched on because one of our engineers thinks that they see a problem with using that and then trying to make a PDF/PS image. Thanks. Rachel Rachel Harte UCSC Genome Bioinformatics Group http://genome.ucsc.edu On Thu, 3 May 2007, Klaus Stark wrote: > Hi Rachel, > > Thank you for your answer. > > I am using MS Windows XP Pro SP2 and Internet Explorer 6.0.2900.2180 as > well as Firefox 2.0.0.3 on a PC with AMD CPU. > > On this machine it worked very well (last download of ps files in > February). > > Best regards, > > Klaus > > > Datum: Thu, 3 May 2007 09:23:50 -0700 (PDT) > Von: Rachel Harte > An: Klaus Stark > Kopie an: genome at soe.ucsc.edu > Betreff: Re: [Genome] problems with export to ps > > > Hello Klaus, > > > > This works ok for me using Mozilla on Linux. However, it may be a > > platform-dependent, browser-dependent problem. Please send us more > > details - which operating system are you using (Windows, Linux) and which > > version? Are you using a PC or a Mac or other machine? Which web browser are > > you using and what version? > > > > With this information, it will be easier for us to figure out what is > > causing the problem? > > > > Thank you. > > > > Rachel > > > > Rachel Harte > > UCSC Genome Bioinformatics Group > > http://genome.ucsc.edu > > > > > > On Thu, 3 May 2007, Klaus Stark wrote: > > > > > Hallo together! > > > > > > You are really doing a good job! > > > But since a few days the export to ps does not function properly. It is > > > always cut on the right side. The phenonemon is independent of the > > > browser used. > > > > > > I hope you can fixed it or help me to solve it locally. > > > > > > Thanks in advance. > > > > > > Best regards, > > > Klaus > > > > > > -- > > > Dr. rer. nat. Klaus Stark > > > Klinik und Poliklinik f?r Innere Medizin II > > > Kardiologie - Forschung > > > Universit?tsklinikum Regensburg > > > Forschungsbau H1 Raum 13 > > > Franz-Josef-Strauss-Allee 11 > > > 93053 Regensburg > > > Tel.: +49-941-944-7340 > > > Fax: +49-941-944-7341 > > > > > > > > > _______________________________________________ > > > Genome maillist - Genome at soe.ucsc.edu > > > http://www.soe.ucsc.edu/mailman/listinfo/genome > > > > > -- > Dr. rer. nat. Klaus Stark > Klinik und Poliklinik f?r Innere Medizin II > Kardiologie - Forschung > Universit?tsklinikum Regensburg > Forschungsbau H1 Raum 13 > Franz-Josef-Strauss-Allee 11 > 93053 Regensburg > Tel.: +49-941-944-7340 > Fax: +49-941-944-7341 > > From jing_gao at agilent.com Thu May 3 12:28:15 2007 From: jing_gao at agilent.com (jing_gao@agilent.com) Date: Thu, 3 May 2007 13:28:15 -0600 Subject: [Genome] question about URL construction Message-ID: <1386D91EC3168B4D9E1F7FA9AE03B25C013B3C14@wcosmb02.cos.agilent.com> Hi, I'm trying to figure out how to construct an URL to share my annotation tracks with others. I'm following your instruction on http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#SHARE, Which works well for human. And I could figure out org=mouse and org=rat. But could you tell me the String values I should use for "org=" in the case for the following species: A. thaliana C. elegans D. melanogaster D. rerio G. gallus H. sapiens human M. musculus mouse R. norvegicus rat S. cerevisiae S. pombe X. tropicalis Thank you very much. Jing From galt at soe.ucsc.edu Thu May 3 13:31:45 2007 From: galt at soe.ucsc.edu (Galt Barber) Date: Thu, 3 May 2007 13:31:45 -0700 (PDT) Subject: [Genome] question about URL construction In-Reply-To: <1386D91EC3168B4D9E1F7FA9AE03B25C013B3C14@wcosmb02.cos.agilent.com> References: <1386D91EC3168B4D9E1F7FA9AE03B25C013B3C14@wcosmb02.cos.agilent.com> Message-ID: Check out name, description, organism, etc. in dbDB in this file: http://hgdownload.cse.ucsc.edu/admin/hgcentral.sql -Galt On Thu, 3 May 2007 jing_gao at agilent.com wrote: > Hi, > > > > I'm trying to figure out how to construct an URL to share my annotation tracks with others. I'm following your instruction on http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#SHARE, > > Which works well for human. And I could figure out org=mouse and org=rat. > > > > But could you tell me the String values I should use for "org=" in the case for the following species: > > > > A. thaliana > > C. elegans > > D. melanogaster > > D. rerio > > G. gallus > > H. sapiens human > > M. musculus mouse > > R. norvegicus rat > > S. cerevisiae > > S. pombe > > X. tropicalis > > > > > > > > Thank you very much. > > > > Jing > > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome > From donnak at soe.ucsc.edu Thu May 3 13:36:56 2007 From: donnak at soe.ucsc.edu (Donna Karolchik) Date: Thu, 3 May 2007 13:36:56 -0700 Subject: [Genome] question about URL construction References: <1386D91EC3168B4D9E1F7FA9AE03B25C013B3C14@wcosmb02.cos.agilent.com> Message-ID: <0b0201c78dc2$cea748f0$0ba8a8c0@donnakLT> hi Jing, To add to what Galt says, if you are using one of the org names that contains white space (e.g. D. melanogaster), be sure to put a "+" in place of the white space, i.e. D.+melanogaster. -Donna ----------------------------------- Donna Karolchik UCSC Genome Bioinformatics Group http://genome.ucsc.edu ----- Original Message ----- From: "Galt Barber" To: Cc: Sent: Thursday, May 03, 2007 1:31 PM Subject: Re: [Genome] question about URL construction > > Check out name, description, organism, etc. in dbDB in this > file: > > http://hgdownload.cse.ucsc.edu/admin/hgcentral.sql > > -Galt > > > On Thu, 3 May 2007 jing_gao at agilent.com wrote: > >> Hi, >> >> >> >> I'm trying to figure out how to construct an URL to share my >> annotation tracks with others. I'm following your instruction >> on >> http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#SHARE, >> >> Which works well for human. And I could figure out org=mouse >> and org=rat. >> >> >> >> But could you tell me the String values I should use for "org=" >> in the case for the following species: >> >> >> >> A. thaliana >> >> C. elegans >> >> D. melanogaster >> >> D. rerio >> >> G. gallus >> >> H. sapiens human >> >> M. musculus mouse >> >> R. norvegicus rat >> >> S. cerevisiae >> >> S. pombe >> >> X. tropicalis >> >> >> >> >> >> >> >> Thank you very much. >> >> >> >> Jing >> >> _______________________________________________ >> Genome maillist - Genome at soe.ucsc.edu >> http://www.soe.ucsc.edu/mailman/listinfo/genome >> > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome > From galt at soe.ucsc.edu Thu May 3 13:40:46 2007 From: galt at soe.ucsc.edu (Galt Barber) Date: Thu, 3 May 2007 13:40:46 -0700 (PDT) Subject: [Genome] question about URL construction In-Reply-To: <0b0201c78dc2$cea748f0$0ba8a8c0@donnakLT> References: <1386D91EC3168B4D9E1F7FA9AE03B25C013B3C14@wcosmb02.cos.agilent.com> <0b0201c78dc2$cea748f0$0ba8a8c0@donnakLT> Message-ID: You can usually just specify the db (e.g. hg18) in the URL (URL=http://server/path/...&db=hg18...), and the system will figure out the org automatically. -Galt On Thu, 3 May 2007, Donna Karolchik wrote: > hi Jing, > > To add to what Galt says, if you are using one of the org names > that contains white space (e.g. D. melanogaster), be sure to put a > "+" in place of the white space, i.e. D.+melanogaster. > > -Donna > ----------------------------------- > Donna Karolchik > UCSC Genome Bioinformatics Group > http://genome.ucsc.edu > > > ----- Original Message ----- > From: "Galt Barber" > To: > Cc: > Sent: Thursday, May 03, 2007 1:31 PM > Subject: Re: [Genome] question about URL construction > > > > > > Check out name, description, organism, etc. in dbDB in this > > file: > > > > http://hgdownload.cse.ucsc.edu/admin/hgcentral.sql > > > > -Galt > > > > > > On Thu, 3 May 2007 jing_gao at agilent.com wrote: > > > >> Hi, > >> > >> > >> > >> I'm trying to figure out how to construct an URL to share my > >> annotation tracks with others. I'm following your instruction > >> on > >> http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#SHARE, > >> > >> Which works well for human. And I could figure out org=mouse > >> and org=rat. > >> > >> > >> > >> But could you tell me the String values I should use for "org=" > >> in the case for the following species: > >> > >> > >> > >> A. thaliana > >> > >> C. elegans > >> > >> D. melanogaster > >> > >> D. rerio > >> > >> G. gallus > >> > >> H. sapiens human > >> > >> M. musculus mouse > >> > >> R. norvegicus rat > >> > >> S. cerevisiae > >> > >> S. pombe > >> > >> X. tropicalis > >> > >> > >> > >> > >> > >> > >> > >> Thank you very much. > >> > >> > >> > >> Jing > >> > >> _______________________________________________ > >> Genome maillist - Genome at soe.ucsc.edu > >> http://www.soe.ucsc.edu/mailman/listinfo/genome > >> > > _______________________________________________ > > Genome maillist - Genome at soe.ucsc.edu > > http://www.soe.ucsc.edu/mailman/listinfo/genome > > > From donnak at soe.ucsc.edu Thu May 3 13:46:40 2007 From: donnak at soe.ucsc.edu (Donna Karolchik) Date: Thu, 3 May 2007 13:46:40 -0700 Subject: [Genome] question about URL construction References: <1386D91EC3168B4D9E1F7FA9AE03B25C013B3C14@wcosmb02.cos.agilent.com><0b0201c78dc2$cea748f0$0ba8a8c0@donnakLT> Message-ID: <0b2201c78dc4$d4796360$0ba8a8c0@donnakLT> You have to be a bit careful when you use the db parameter -- it depends on what you want from your URL. If you want the URL to always point to that specific assembly version, it's better to use the db name. However, if you want your URL to always point to the latest assembly version for a genome (i.e. automatically use the newer version if an assembly is updated), then you should use the org name. -Donna ----- Original Message ----- From: "Galt Barber" To: "Donna Karolchik" Cc: ; Sent: Thursday, May 03, 2007 1:40 PM Subject: Re: [Genome] question about URL construction > > You can usually just specify the db (e.g. hg18) in the URL > (URL=http://server/path/...&db=hg18...), and the system > will figure out the org automatically. > > -Galt > > > On Thu, 3 May 2007, Donna Karolchik wrote: > >> hi Jing, >> >> To add to what Galt says, if you are using one of the org names >> that contains white space (e.g. D. melanogaster), be sure to >> put a >> "+" in place of the white space, i.e. D.+melanogaster. >> >> -Donna >> ----------------------------------- >> Donna Karolchik >> UCSC Genome Bioinformatics Group >> http://genome.ucsc.edu >> >> >> ----- Original Message ----- >> From: "Galt Barber" >> To: >> Cc: >> Sent: Thursday, May 03, 2007 1:31 PM >> Subject: Re: [Genome] question about URL construction >> >> >> > >> > Check out name, description, organism, etc. in dbDB in this >> > file: >> > >> > http://hgdownload.cse.ucsc.edu/admin/hgcentral.sql >> > >> > -Galt >> > >> > >> > On Thu, 3 May 2007 jing_gao at agilent.com wrote: >> > >> >> Hi, >> >> >> >> >> >> >> >> I'm trying to figure out how to construct an URL to share my >> >> annotation tracks with others. I'm following your >> >> instruction >> >> on >> >> http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#SHARE, >> >> >> >> Which works well for human. And I could figure out org=mouse >> >> and org=rat. >> >> >> >> >> >> >> >> But could you tell me the String values I should use for >> >> "org=" >> >> in the case for the following species: >> >> >> >> >> >> >> >> A. thaliana >> >> >> >> C. elegans >> >> >> >> D. melanogaster >> >> >> >> D. rerio >> >> >> >> G. gallus >> >> >> >> H. sapiens human >> >> >> >> M. musculus mouse >> >> >> >> R. norvegicus rat >> >> >> >> S. cerevisiae >> >> >> >> S. pombe >> >> >> >> X. tropicalis >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> Thank you very much. >> >> >> >> >> >> >> >> Jing >> >> >> >> _______________________________________________ >> >> Genome maillist - Genome at soe.ucsc.edu >> >> http://www.soe.ucsc.edu/mailman/listinfo/genome >> >> >> > _______________________________________________ >> > Genome maillist - Genome at soe.ucsc.edu >> > http://www.soe.ucsc.edu/mailman/listinfo/genome >> > >> > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome > From jing_gao at agilent.com Thu May 3 13:54:23 2007 From: jing_gao at agilent.com (jing_gao@agilent.com) Date: Thu, 3 May 2007 14:54:23 -0600 Subject: [Genome] question about URL construction In-Reply-To: <0b2201c78dc4$d4796360$0ba8a8c0@donnakLT> Message-ID: <1386D91EC3168B4D9E1F7FA9AE03B25C013B3C5D@wcosmb02.cos.agilent.com> Hi, Thanks for the help, I tried "org=S.+cerevisiae" and it works now. I do want to always point to the latest version. I think I can get the rest of the information from the table. Thank you so much, Jing -----Original Message----- From: Donna Karolchik [mailto:donnak at soe.ucsc.edu] Sent: Thursday, May 03, 2007 1:47 PM To: Galt Barber Cc: jing_gao at agilent.com; Genome Subject: Re: [Genome] question about URL construction You have to be a bit careful when you use the db parameter -- it depends on what you want from your URL. If you want the URL to always point to that specific assembly version, it's better to use the db name. However, if you want your URL to always point to the latest assembly version for a genome (i.e. automatically use the newer version if an assembly is updated), then you should use the org name. -Donna ----- Original Message ----- From: "Galt Barber" To: "Donna Karolchik" Cc: ; Sent: Thursday, May 03, 2007 1:40 PM Subject: Re: [Genome] question about URL construction > > You can usually just specify the db (e.g. hg18) in the URL > (URL=http://server/path/...&db=hg18...), and the system > will figure out the org automatically. > > -Galt > > > On Thu, 3 May 2007, Donna Karolchik wrote: > >> hi Jing, >> >> To add to what Galt says, if you are using one of the org names >> that contains white space (e.g. D. melanogaster), be sure to >> put a >> "+" in place of the white space, i.e. D.+melanogaster. >> >> -Donna >> ----------------------------------- >> Donna Karolchik >> UCSC Genome Bioinformatics Group >> http://genome.ucsc.edu >> >> >> ----- Original Message ----- >> From: "Galt Barber" >> To: >> Cc: >> Sent: Thursday, May 03, 2007 1:31 PM >> Subject: Re: [Genome] question about URL construction >> >> >> > >> > Check out name, description, organism, etc. in dbDB in this >> > file: >> > >> > http://hgdownload.cse.ucsc.edu/admin/hgcentral.sql >> > >> > -Galt >> > >> > >> > On Thu, 3 May 2007 jing_gao at agilent.com wrote: >> > >> >> Hi, >> >> >> >> >> >> >> >> I'm trying to figure out how to construct an URL to share my >> >> annotation tracks with others. I'm following your >> >> instruction >> >> on >> >> http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#SHARE, >> >> >> >> Which works well for human. And I could figure out org=mouse >> >> and org=rat. >> >> >> >> >> >> >> >> But could you tell me the String values I should use for >> >> "org=" >> >> in the case for the following species: >> >> >> >> >> >> >> >> A. thaliana >> >> >> >> C. elegans >> >> >> >> D. melanogaster >> >> >> >> D. rerio >> >> >> >> G. gallus >> >> >> >> H. sapiens human >> >> >> >> M. musculus mouse >> >> >> >> R. norvegicus rat >> >> >> >> S. cerevisiae >> >> >> >> S. pombe >> >> >> >> X. tropicalis >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> Thank you very much. >> >> >> >> >> >> >> >> Jing >> >> >> >> _______________________________________________ >> >> Genome maillist - Genome at soe.ucsc.edu >> >> http://www.soe.ucsc.edu/mailman/listinfo/genome >> >> >> > _______________________________________________ >> > Genome maillist - Genome at soe.ucsc.edu >> > http://www.soe.ucsc.edu/mailman/listinfo/genome >> > >> > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome > From aindap at yahoo.com Thu May 3 14:21:59 2007 From: aindap at yahoo.com (Amit Indap) Date: Thu, 3 May 2007 14:21:59 -0700 (PDT) Subject: [Genome] exon frame in genepred files Message-ID: <759127.473.qm@web32611.mail.mud.yahoo.com> Hi UCSC I was looking at this message where Ann did a great job explaining what exactly the exon frame fields mean in genepred files. http://www.soe.ucsc.edu/pipermail/genome/2006-November/012218.html Pardon me if this is a silly question, but why couldn't you just do (exonEnd-exonStart) % 3 to get the frame? If the modulus result isn't 3, then does the exon pick up the extra nucleotides from the next exon in the list or the exon before it? Thanks for the help! Amit Indap Cornell University __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From archanat at soe.ucsc.edu Thu May 3 15:24:29 2007 From: archanat at soe.ucsc.edu (Archana Thakkapallayil) Date: Thu, 03 May 2007 15:24:29 -0700 Subject: [Genome] exon frame in genepred files In-Reply-To: <759127.473.qm@web32611.mail.mud.yahoo.com> References: <759127.473.qm@web32611.mail.mud.yahoo.com> Message-ID: <463A611D.9090302@soe.ucsc.edu> Hello Amit, Here is the response from one of our developers: There are several reasons why the frame in the annotation might not match what one would compute using mod 3 (counting codons): - translational frame shifts; some genes have bases in the mRNA that are skipped during translation. - sequencing error in the mRNA or genome - polymorphism; the mRNA might be from an individual that has a frame shift polymorphism compared to the reference genome. I hope this information is helpful to you. If you have further questions, please do not hesitate to contact us again. Regards, Archana UCSC Genome Bioinformatics Group We invite you to give us your feedback on the UCSC Genome Browser through May 31, 2007: http://www.surveymonkey.com/s.asp?U=881163743177 Amit Indap wrote: > Hi UCSC > > I was looking at this message where Ann did a great > job explaining what exactly the exon frame fields mean > in genepred files. > > http://www.soe.ucsc.edu/pipermail/genome/2006-November/012218.html > > Pardon me if this is a silly question, but why > couldn't you just do (exonEnd-exonStart) % 3 to get > the frame? > > If the modulus result isn't 3, then does the exon pick > up the extra nucleotides from the next exon in the > list or the exon before it? > > Thanks for the help! > > Amit Indap > Cornell University > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome > From Adam.Ameur at lcb.uu.se Fri May 4 04:49:16 2007 From: Adam.Ameur at lcb.uu.se (Adam Ameur) Date: Fri, 4 May 2007 13:49:16 +0200 Subject: [Genome] track submission request Message-ID: <5B18CDA9-A752-4226-B3F4-5DEFB3B717F2@lcb.uu.se> Hi, I am working in Claes Wadelius' group at Uppsala University, Sweden. We have previously submitted tracks for two ChIP-chip experiments on ENCODE regions. Now we have new results for the whole human genome using Affymetrix high density arrays with 35 bp resolution. This time we have studied two transcription factors (USF1 and USF2) as well as acetylation of histone 3. We will submit a manuscript in a few weeks and would like to know if it is possible to make our data available from the UCSC browser. If so, we have to decide if we can present all of the data (there are millions of data points) or only the regions that we define as positives. Your advice on this matter is highly appreciated. Best regards, Adam Ameur From dianasantacruz at gmail.com Fri May 4 02:51:07 2007 From: dianasantacruz at gmail.com (diana santacruz) Date: Fri, 4 May 2007 11:51:07 +0200 Subject: [Genome] link for custom track does not work Message-ID: <913730430705040251j50a225b3vd40318a15f49cbaa@mail.gmail.com> Hello UCSC-Browser: I have a list of data that I want to visualize int he genome browser. For each item of the list (gene) I would like to have a direct link that shows the exact position along with my custom tracks. For this I made a test with the following link: http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg17&position=chr21:13000000-14000000&hgt.customText=http://www.uni-saarland.de/fak8/genetik/rawdata/2007_02_20_poster_exam.bed It takes a bit to open and when it does it shows the whole chromosome 21 rather than the specified position. Could you please tell me if I have done something wrong and why it is not working? Thank you very much. -- Diana From fstvirol at zedat.fu-berlin.de Fri May 4 05:11:42 2007 From: fstvirol at zedat.fu-berlin.de (Dr Falko Steinbach) Date: Fri, 4 May 2007 13:11:42 +0100 Subject: [Genome] horse genome Message-ID: <07B3C611-A0F8-4D4E-970B-B003E531C6F9@zedat.fu-berlin.de> Dear genome, I have come across the page http://hgdownload.cse.ucsc.edu/goldenPath/ equCab1/bigZips/ with some interest. The description provides info on all the genome files, but from the names such as est, mrna or refmrna, I conclude there are other information available as well. Could you provide information what that is, who collated or alike. Regards Falko ############################## PD Dr. Falko Steinbach Mammalian Virology Group Veterinary Laboratories Agency - Weybridge New Haw, Addlestone, Surrey KT15 3NB United Kingdom Direct Line +44 (0) 1932 357566 Facsimile +44 (0) 1932 357239 E-mail f.steinbach at vla.defra.gsi.gov.uk ############################### From fanhsu at soe.ucsc.edu Fri May 4 10:02:02 2007 From: fanhsu at soe.ucsc.edu (Fan Hsu) Date: Fri, 4 May 2007 10:02:02 -0700 Subject: [Genome] horse genome In-Reply-To: <07B3C611-A0F8-4D4E-970B-B003E531C6F9@zedat.fu-berlin.de> Message-ID: Hi Falko, We are in the process of releasing the horse (equCab1) genome. The files you saw are downloadable files we put out as part of the preparation of our coming public equCab1 release. In the mean time, you can have a preview of the horse genome browser at our internal test server at: http://genome-test.cse.ucsc.edu/cgi-bin/hgGateway?db=equCab1 Fan. -----Original Message----- From: genome-bounces at soe.ucsc.edu [mailto:genome-bounces at soe.ucsc.edu]On Behalf Of Dr Falko Steinbach Sent: Friday, May 04, 2007 5:12 AM To: genome at soe.ucsc.edu Subject: [Genome] horse genome Dear genome, I have come across the page http://hgdownload.cse.ucsc.edu/goldenPath/ equCab1/bigZips/ with some interest. The description provides info on all the genome files, but from the names such as est, mrna or refmrna, I conclude there are other information available as well. Could you provide information what that is, who collated or alike. Regards Falko ############################## PD Dr. Falko Steinbach Mammalian Virology Group Veterinary Laboratories Agency - Weybridge New Haw, Addlestone, Surrey KT15 3NB United Kingdom Direct Line +44 (0) 1932 357566 Facsimile +44 (0) 1932 357239 E-mail f.steinbach at vla.defra.gsi.gov.uk ############################### _______________________________________________ Genome maillist - Genome at soe.ucsc.edu http://www.soe.ucsc.edu/mailman/listinfo/genome From kate at soe.ucsc.edu Fri May 4 10:03:34 2007 From: kate at soe.ucsc.edu (Kate Rosenbloom) Date: Fri, 4 May 2007 10:03:34 -0700 Subject: [Genome] track submission request In-Reply-To: <5B18CDA9-A752-4226-B3F4-5DEFB3B717F2@lcb.uu.se> References: <5B18CDA9-A752-4226-B3F4-5DEFB3B717F2@lcb.uu.se> Message-ID: Hello Adam, If this is ENCODE-funded experimental data, we would need the probe-level or smoothed data as well as the identified positive regions. If not, we should discuss further off-line. We are definitely interested in hosting additional whole-genome Chip/chip data. Cheers, Kate --- Kate Rosenbloom UCSC Genome Bioinformatics On May 4, 2007, at 4:49 AM, Adam Ameur wrote: > Hi, > > I am working in Claes Wadelius' group at Uppsala University, Sweden. > We have previously submitted tracks for two ChIP-chip experiments on > ENCODE regions. Now we have new results for the whole human genome > using Affymetrix high density arrays with 35 bp resolution. This time > we have studied two transcription factors (USF1 and USF2) as well as > acetylation of histone 3. > > We will submit a manuscript in a few weeks and would like to know if > it is possible to make our data available from the UCSC browser. If > so, we have to decide if we can present all of the data (there are > millions of data points) or only the regions that we define as > positives. > > Your advice on this matter is highly appreciated. > > Best regards, > Adam Ameur > > > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome From hiram at soe.ucsc.edu Fri May 4 10:14:44 2007 From: hiram at soe.ucsc.edu (Hiram Clawson) Date: Fri, 04 May 2007 10:14:44 -0700 Subject: [Genome] link for custom track does not work In-Reply-To: <913730430705040251j50a225b3vd40318a15f49cbaa@mail.gmail.com> References: <913730430705040251j50a225b3vd40318a15f49cbaa@mail.gmail.com> Message-ID: <463B6A04.3030406@soe.ucsc.edu> Good Morning Diana: The reason the browser opens to the entire chr21 is because you have the line: browser position chr21 at the top of your data file. This position specification overrides the position specification you have in your URL. Either eliminate this data line from your file, or set it to be the position you want this data to start out on in the browser. --Hiram diana santacruz wrote: > Hello UCSC-Browser: > > I have a list of data that I want to visualize int he genome browser. > For each item of the list (gene) I would like to have a direct link > that shows the exact position along with my custom tracks. > > For this I made a test with the following link: > > http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg17&position=chr21:13000000-14000000&hgt.customText=http://www.uni-saarland.de/fak8/genetik/rawdata/2007_02_20_poster_exam.bed > > It takes a bit to open and when it does it shows the whole chromosome > 21 rather than the specified position. > > Could you please tell me if I have done something wrong and why it is > not working? > > Thank you very much. From rhead at soe.ucsc.edu Fri May 4 10:15:17 2007 From: rhead at soe.ucsc.edu (Brooke Rhead) Date: Fri, 04 May 2007 10:15:17 -0700 Subject: [Genome] link for custom track does not work In-Reply-To: <913730430705040251j50a225b3vd40318a15f49cbaa@mail.gmail.com> References: <913730430705040251j50a225b3vd40318a15f49cbaa@mail.gmail.com> Message-ID: <463B6A25.7030202@soe.ucsc.edu> Hello Diana, It appears that there is also a position specified in your data file ("browser position 21") that is overwriting the position given in the URL. If you remove the position in the file, this should resolve the problem. Let us know if this does not work, or if you have further questions. -- Brooke Rhead UCSC Genome Bioinformatics Group diana santacruz wrote: > Hello UCSC-Browser: > > I have a list of data that I want to visualize int he genome browser. > For each item of the list (gene) I would like to have a direct link > that shows the exact position along with my custom tracks. > > For this I made a test with the following link: > > http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&db=hg17&position=chr21:13000000-14000000&hgt.customText=http://www.uni-saarland.de/fak8/genetik/rawdata/2007_02_20_poster_exam.bed > > It takes a bit to open and when it does it shows the whole chromosome > 21 rather than the specified position. > > Could you please tell me if I have done something wrong and why it is > not working? > > Thank you very much. > > From szhao3 at ncsu.edu Fri May 4 12:15:50 2007 From: szhao3 at ncsu.edu (szhao3@ncsu.edu) Date: Fri, 4 May 2007 15:15:50 -0400 (EDT) Subject: [Genome] Find conservation scores for transcripts Message-ID: <2858.152.14.14.82.1178306150.squirrel@webmail.ncsu.edu> Hello, Is there a fast way to get the conservation scores of a set of transcripts, including the intronic regions? Thanks a lot. Sihui Zhao From hartera at soe.ucsc.edu Fri May 4 13:29:42 2007 From: hartera at soe.ucsc.edu (Rachel Harte) Date: Fri, 4 May 2007 13:29:42 -0700 (PDT) Subject: [Genome] problems with export to ps In-Reply-To: <463A2A75.26946.1E4DDCB@klaus.stark.klinik.uni-regensburg.de> References: <4639BEDD.2081.409534@klaus.stark.klinik.uni-regensburg.de> <463A2A75.26946.1E4DDCB@klaus.stark.klinik.uni-regensburg.de> Message-ID: Klaus, As you may have seen from an earlier message, a fix has been made to correct the PostScript problem that you were seeing. Unfortunately, we have not been able to incorporate into our latest software build, but you can use the corrected version on our development server: http://genome-test.cse.ucsc.edu Please note that any date on this server that is not on the public server may not have been tested yet and may therefore change before being released to the public web site. In two weeks, the fix to this problem will be incorporated into the software build used on the public servers. Rachel Rachel Harte UCSC Genome Bioinformatics Group http://genome.ucsc.edu On Thu, 3 May 2007, Klaus Stark wrote: > Hi Rachel, > > Thank you for your answer. > > I am using MS Windows XP Pro SP2 and Internet Explorer 6.0.2900.2180 as > well as Firefox 2.0.0.3 on a PC with AMD CPU. > > On this machine it worked very well (last download of ps files in > February). > > Best regards, > > Klaus > > > Datum: Thu, 3 May 2007 09:23:50 -0700 (PDT) > Von: Rachel Harte > An: Klaus Stark > Kopie an: genome at soe.ucsc.edu > Betreff: Re: [Genome] problems with export to ps > > > Hello Klaus, > > > > This works ok for me using Mozilla on Linux. However, it may be a > > platform-dependent, browser-dependent problem. Please send us more > > details - which operating system are you using (Windows, Linux) and which > > version? Are you using a PC or a Mac or other machine? Which web browser are > > you using and what version? > > > > With this information, it will be easier for us to figure out what is > > causing the problem? > > > > Thank you. > > > > Rachel > > > > Rachel Harte > > UCSC Genome Bioinformatics Group > > http://genome.ucsc.edu > > > > > > On Thu, 3 May 2007, Klaus Stark wrote: > > > > > Hallo together! > > > > > > You are really doing a good job! > > > But since a few days the export to ps does not function properly. It is > > > always cut on the right side. The phenonemon is independent of the > > > browser used. > > > > > > I hope you can fixed it or help me to solve it locally. > > > > > > Thanks in advance. > > > > > > Best regards, > > > Klaus > > > > > > -- > > > Dr. rer. nat. Klaus Stark > > > Klinik und Poliklinik f?r Innere Medizin II > > > Kardiologie - Forschung > > > Universit?tsklinikum Regensburg > > > Forschungsbau H1 Raum 13 > > > Franz-Josef-Strauss-Allee 11 > > > 93053 Regensburg > > > Tel.: +49-941-944-7340 > > > Fax: +49-941-944-7341 > > > > > > > > > _______________________________________________ > > > Genome maillist - Genome at soe.ucsc.edu > > > http://www.soe.ucsc.edu/mailman/listinfo/genome > > > > > -- > Dr. rer. nat. Klaus Stark > Klinik und Poliklinik f?r Innere Medizin II > Kardiologie - Forschung > Universit?tsklinikum Regensburg > Forschungsbau H1 Raum 13 > Franz-Josef-Strauss-Allee 11 > 93053 Regensburg > Tel.: +49-941-944-7340 > Fax: +49-941-944-7341 > > From dinghs at hotmail.com Fri May 4 12:44:27 2007 From: dinghs at hotmail.com (Huashi Ding) Date: Fri, 04 May 2007 19:44:27 +0000 Subject: [Genome] high volumn of traffic Message-ID: Hello, I have ~1200 sequences, each one is 25-mer. I'd like to use BLAT search. I'm using a script but got the following message. I was wondering is there a more efficient way to do that? (Actually I have another no-so-urgent batch with ~20000 25-mer sequences, I know I can't ask too much :) Thanks and best regards, -Ding ----------------------------------------------------------------- There is a very high volume of traffic coming from your site (IP address 70.255.34.102) as of Fri May 4 08:00:31 2007 (California time). So that other users get a fair share of our bandwidth, we are putting in a delay of 10.3 seconds before we service your request. This delay will slowly decrease over a half hour as activity returns to normal. This high volume of traffic is likely due to program-driven rather than interactive access, or the submission of queries on a large number of sequences. If you are making large batch queries, please write to our genome at cse.ucsc.edu public mailing list and inquire about more efficient ways to access our data. If you are sharing an IP address with someone who is sumitting large batch queries, we apologize for the inconvenience. Please contact genome-www at cse.ucsc.edu if you think this delay is being imposed unfairly. ----------------------------------------------------------------- _________________________________________________________________ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ From rhead at soe.ucsc.edu Fri May 4 14:25:53 2007 From: rhead at soe.ucsc.edu (Brooke Rhead) Date: Fri, 04 May 2007 14:25:53 -0700 Subject: [Genome] high volumn of traffic In-Reply-To: References: Message-ID: <463BA4E1.4020307@soe.ucsc.edu> Hi Ding, From our BLAT FAQ page http://genome.ucsc.edu/FAQ/FAQblat.html : Due to the high demand on our Blat servers, we restrict service for users who programatically query Blat or do large batch queries. Program-driven use of Blat is limited to a maximum of one hit every 15 seconds and no more than 5,000 hits per day. Please limit batch queries to 25 sequences or less. So, if you slow down the hits to our site from your script to once every 15 seconds, you should be able to complete your job. Alternatively, if you have the facilities to set up your own BLAT server, that is the most efficient way to go about completing large jobs. BLAT sources and executables are free for academic, personal, and non-profit use. More information on setting up a local BLAT server is available in the BLAT FAQs (linked above) and in the BLAT section of the Genome Browser Users Guide: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BLATAlign . I hope this information helps. -- Brooke Rhead UCSC Genome Bioinformatics Group Huashi Ding wrote: > Hello, > > I have ~1200 sequences, each one is 25-mer. I'd like to use BLAT search. I'm > using a script but got the following message. I was wondering is there a > more efficient way to do that? > > (Actually I have another no-so-urgent batch with ~20000 25-mer sequences, I > know I can't ask too much :) > > Thanks and best regards, > -Ding > > ----------------------------------------------------------------- > There is a very high volume of traffic coming from your site (IP address > 70.255.34.102) as of Fri May 4 08:00:31 2007 (California time). So that > other users get a fair share of our bandwidth, we are putting in a delay of > 10.3 seconds before we service your request. This delay will slowly decrease > over a half hour as activity returns to normal. This high volume of traffic > is likely due to program-driven rather than interactive access, or the > submission of queries on a large number of sequences. If you are making > large batch queries, please write to our genome at cse.ucsc.edu public mailing > list and inquire about more efficient ways to access our data. If you are > sharing an IP address with someone who is sumitting large batch queries, we > apologize for the inconvenience. Please contact genome-www at cse.ucsc.edu if > you think this delay is being imposed unfairly. > ----------------------------------------------------------------- > > _________________________________________________________________ > Express yourself instantly with MSN Messenger! Download today it's FREE! > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ > > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome From rhead at soe.ucsc.edu Fri May 4 15:11:13 2007 From: rhead at soe.ucsc.edu (Brooke Rhead) Date: Fri, 04 May 2007 15:11:13 -0700 Subject: [Genome] Find conservation scores for transcripts In-Reply-To: <2858.152.14.14.82.1178306150.squirrel@webmail.ncsu.edu> References: <2858.152.14.14.82.1178306150.squirrel@webmail.ncsu.edu> Message-ID: <463BAF81.4010002@soe.ucsc.edu> Hello Sihui, It is possible to retrieve conservation scores for one or two particular transcripts by using the Table Browser. To do this, select the "phastCons*way" table from the appropriate database, then intersect that table with a custom track of the transcripts, and choose "data points" as the output. However, because conservation score data is quite large (one data point for each base), the Table Browser method is impractical for more than a few transcripts. Instead, you can download conservation scores for an entire genome (or just the chromosomes of interest), and extract scores for just your ranges of interest. The phastCons score downloads are available on our downloads server: http://hgdownload.cse.ucsc.edu/downloads.html The phastCons file format is described here (note that position coordinates are 1-based, unlike most of our other data formats, which are 0-based): http://genome.ucsc.edu/goldenPath/help/phastCons.html I hope this information helps. If you have further questions, please feel free to write back to this list. -- Brooke Rhead UCSC Genome Bioinformatics Group We invite you to give us your feedback on the UCSC Genome Browser through May 31, 2007: http://www.surveymonkey.com/s.asp?U=881163743177 szhao3 at ncsu.edu wrote: > Hello, > > Is there a fast way to get the conservation scores of a set of > transcripts, including the intronic regions? Thanks a lot. > > Sihui Zhao > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome From carrk at msu.edu Fri May 4 14:53:34 2007 From: carrk at msu.edu (Kevin M. Carr) Date: Fri, 04 May 2007 17:53:34 -0400 Subject: [Genome] BLAT gives wrong tStarts for translated searches. Message-ID: Hello all, I am attempting to align RefSeq mRNA sequences from related species to an in-house draft genome assembly. I am doing the alignment in protein space with the -t=dnax and -q=rnax. While the results for alignments to the + strand appear normal I am getting incorrect (or at least confusing) output for alignments to the - strand of the target. More specifically the individual tStarts locations do not fall within the T start and T end positions given. Here is and example: psLayout version 3 match mis- rep. N's Q gap Q gap T gap T gap strand Q Q Q Q T T T T block blockSizes qStarts tStarts match match count bases count bases name size start end name size start end count ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- ------- 442 122 0 0 3 951 3 846 +- SINFRUT00000182842 1599 78 1593 stig_26 225935 221426 222836 4 180,228,36,120, 78,288,552,1473, 3099,3330,3585,4389, As can be seen, the T start is 221426 and T end is 222836 but the tStarts are given as 3099,3330,3585,4389 It seems that every alignment to the - strand is incorrect while every one to the + strand seems fine. I have run this using command line BLAT (32X1) and gfServer/gfClient (33X7) (gfServer started with -trans and gfClient run with -q=rnax) and the results are the same either way. Am I missing something? Insights and suggestions greatly appreciated. Kevin M. Carr ************************** Bioinformatics Specialist Research Technology Support Facility 202-D Biochemistry Bldg. Michigan State University East Lansing, MI 48824 Ph: (517) 353-6794 Fax:(517) 353-8638 ************************** From wenocur at genome.chop.edu Sun May 6 20:21:12 2007 From: wenocur at genome.chop.edu (Adam Wenocur) Date: Sun, 06 May 2007 23:21:12 -0400 Subject: [Genome] memory leaks in cartCheckout Message-ID: Hi all, I was recently poking around the heap of the genome browser CGI executables, and I noticed some peculiarities. Upon further inspection, I found that the cartCheckout function in kent/src/hg/lib/cart.c is the source of some memory leaks: Instead of calling freeHash, cartCheckout should call freeHashAndVals, since the values loaded into the cart are cloned strings, and are otherwise orphaned. There is the possibility that this solution might break the use of cart parameter strings that were not copied prior to checking out the cart, however it seems not to have caused any ill effect on my genome browser mirror. A second issue doesn't appear to be causing leaks, but may have the potential to: cartCheckout should use cartDbFreeList instead cartDbFree, since userInfo and sessionInfo are indirectly assigned by cartDbLoadWhere in cartNew, and could point to linked lists. I'm aware that this isn't of great importance to the CGI binaries, since cartCheckout is usually called shortly before a program exits, but I figure it couldn't hurt to note my observations. -Adam From ajones at cshl.edu Mon May 7 07:36:18 2007 From: ajones at cshl.edu (Jones, Adrienne) Date: Mon, 07 May 2007 10:36:18 -0400 Subject: [Genome] Message-ID: Hello, How can I view all of the nucleotide sequence showing all of the alternatively spliced isoforms for a given gene? Thank you for your time and help. From daniel.gaffney at mcgill.ca Mon May 7 09:50:04 2007 From: daniel.gaffney at mcgill.ca (Daniel Gaffney) Date: Mon, 07 May 2007 12:50:04 -0400 Subject: [Genome] Chimp assembly 2 pairwise alignments Message-ID: <463F58BC.8050306@mcgill.ca> Hi there, I have ~ 1500 small regions in the human genome, for which I would like to get the human-chimp pairwise alignment for the latest chimp assembly. However, I'm having a little trouble in figuring out the best way to do this - can this be done locally? Or is there a batch submission tool that I can retrieve all alignments from UCSC directly - I've tried the table browser, but I can't seem to get the specific region I want (i.e. if i select the chimp chain track, and retrieve sequence, I get the the alignment of that entire region, not just the region corresponding to the coordinates I've entered). Any ideas? Cheers Dan -- ================================================================ Daniel Gaffney McGill University and Genome Quebec Innovation Centre 740 ave Dr Penfield Rm 7208 Montreal (Quebec) H3A 1A4 http://dutch.cap.ed.ac.uk/ Tel: +1 514 398 3311 ext: 04592 Fax: +1 514 398 1790 ================================================================ From archanat at soe.ucsc.edu Mon May 7 11:17:27 2007 From: archanat at soe.ucsc.edu (Archana Thakkapallayil) Date: Mon, 07 May 2007 11:17:27 -0700 Subject: [Genome] In-Reply-To: References: Message-ID: <463F6D37.7040605@soe.ucsc.edu> Hello Adrienne, You could get this information using the Table Browser. To get to this make the following selections in the Table Browser: clade: vertebrate genome: human assembly: Mar. 2006 group: Genes and Gene Prediction Tracks track: UCSC Genes table: kgXref click on "filter: create" button and then paste your gene name into the geneSymbol text box.( If you have a list of genes you can paste the white-space separated list of gene names into the geneSymbol text box ) then click "submit" . Set output format: "selected fields from primary and related tables", then click "get output". Then select the field 'kgId' and hit "get output". This gives you the ucsc id's for all the isoforms for your gene of interest. You could then use the Table Browser on 'knownGene' table and then paste or upload your list of known gene id's using the paste/upload list feature. You can then choose 'sequence' as output format. This gives you the sequence for each isoform. I hope this information is helpful to you. Please let us know if you have further questions. Regards, Archana UCSC genome Bioinformatics Group Jones, Adrienne wrote: > Hello, > > How can I view all of the nucleotide sequence showing all of the > alternatively spliced isoforms for a given gene? > > Thank you for your time and help. > > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome > From galt at soe.ucsc.edu Mon May 7 11:21:56 2007 From: galt at soe.ucsc.edu (Galt Barber) Date: Mon, 7 May 2007 11:21:56 -0700 (PDT) Subject: [Genome] BLAT gives wrong tStarts for translated searches. In-Reply-To: References: Message-ID: Hi, Kevin http://hgwdev.cse.ucsc.edu/goldenPath/help/hgTracksHelp.html#PSL Read through, paying particular attention to the bits about "negative strand" and "minus strand". Here are a couple of quotes that may be useful: "Be aware that the coordinates for a negative strand in a PSL line are handled in a special way. In the qStart and qEnd fields, the coordinates indicate the position where the query matches from the point of view of the forward strand, even when the match is on the reverse strand. However, in the qStarts list, the coordinates are reversed." "Essentially, the minus strand blockSizes and qStarts are what you would get if you reverse-complemented the query. However, the qStart and qEnd are not reversed. To convert one to the other: qStart = qSize - revQEnd qEnd = qSize - revQStart " Good Luck! -Galt On Fri, 4 May 2007, Kevin M. Carr wrote: > Hello all, > > I am attempting to align RefSeq mRNA sequences from related species to an > in-house draft genome assembly. I am doing the alignment in protein space > with the -t=dnax and -q=rnax. While the results for alignments to the + > strand appear normal I am getting incorrect (or at least confusing) output > for alignments to the - strand of the target. More specifically the > individual tStarts locations do not fall within the T start and T end > positions given. Here is and example: > > psLayout version 3 > > match mis- rep. N's Q gap Q gap T gap T gap strand Q > Q Q Q T T T T block > blockSizes qStarts tStarts > match match count bases count bases name > size start end name size start end count > ---------------------------------------------------------------------------- > ---------------------------------------------------------------------------- > ------- > 442 122 0 0 3 951 3 846 +- > SINFRUT00000182842 1599 78 1593 stig_26 225935 221426 > 222836 4 180,228,36,120, 78,288,552,1473, > 3099,3330,3585,4389, > > As can be seen, the T start is 221426 and T end is 222836 but the tStarts > are given as 3099,3330,3585,4389 > > It seems that every alignment to the - strand is incorrect while every one > to the + strand seems fine. I have run this using command line BLAT (32X1) > and gfServer/gfClient (33X7) (gfServer started with -trans and gfClient run > with -q=rnax) and the results are the same either way. > > Am I missing something? > > Insights and suggestions greatly appreciated. > > Kevin M. Carr > > ************************** > Bioinformatics Specialist > Research Technology > Support Facility > 202-D Biochemistry Bldg. > Michigan State University > East Lansing, MI 48824 > > Ph: (517) 353-6794 > Fax:(517) 353-8638 > ************************** > > > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome > From rosenfel at cshl.edu Mon May 7 10:16:19 2007 From: rosenfel at cshl.edu (Jeffrey Rosenfeld) Date: Mon, 07 May 2007 13:16:19 -0400 Subject: [Genome] knownIsoforms Message-ID: <463F5EE3.1040600@cshl.edu> How is the knownisoforms table constructed? It seems that all overlapping genes are clustered together, but there are examples, such as at the very beginning of chromosome 1, where a transcript within a cluster becomes its own cluster. When I run the following query on hg18: select clusterID,name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd from knownIsoforms, knownGene where transcript = name; These are the results I get: | clusterID | name | chrom | strand | txStart | txEnd | cdsStart | cdsEnd | +-----------+------------+-------+--------+---------+--------+----------+--------+ | 1 | uc001aaa.1 | chr1 | + | 1736 | 4121 | 1736 | 1736 | | 2 | uc001aab.1 | chr1 | - | 4558 | 14764 | 4558 | 4558 | | 2 | uc001aac.1 | chr1 | - | 4558 | 19346 | 4558 | 4558 | | 2 | uc001aad.1 | chr1 | - | 4558 | 7231 | 4558 | 7173 | | 2 | uc001aae.1 | chr1 | - | 4558 | 9622 | 4558 | 4558 | | 2 | uc001aaf.1 | chr1 | - | 4832 | 19672 | 4832 | 4832 | | 2 | uc001aag.1 | chr1 | - | 5658 | 7231 | 5658 | 5658 | | 2 | uc001aah.1 | chr1 | - | 6720 | 19346 | 6720 | 6720 | | 2 | uc001aai.1 | chr1 | - | 6720 | 9622 | 6720 | 6720 | | 3 | uc001aaj.1 | chr1 | - | 7777 | 19346 | 7777 | 14749 | Shouldn't cluster 3 be included as part of cluster 4? Thank You, Jeffrey Rosenfeld From fanhsu at soe.ucsc.edu Mon May 7 11:38:32 2007 From: fanhsu at soe.ucsc.edu (Fan Hsu) Date: Mon, 7 May 2007 11:38:32 -0700 Subject: [Genome] knownIsoforms In-Reply-To: <463F5EE3.1040600@cshl.edu> Message-ID: Hi Jeff, The knownisoforms table is generated by a program txGeneCanonical, written by Jim Kent. Jim is out of town today, not sure he has email access or not. My guess is that this program first identifies overlapping genes and then find the longest one and designate it as the representative canonical gene of the cluster. In the mean time, you can find the details of this program by downloading our src tree and find this program under: kent/src/hg/txGene/txGeneCanonical Fan. -----Original Message----- From: genome-bounces at soe.ucsc.edu [mailto:genome-bounces at soe.ucsc.edu]On Behalf Of Jeffrey Rosenfeld Sent: Monday, May 07, 2007 10:16 AM To: genome at soe.ucsc.edu Subject: [Genome] knownIsoforms How is the knownisoforms table constructed? It seems that all overlapping genes are clustered together, but there are examples, such as at the very beginning of chromosome 1, where a transcript within a cluster becomes its own cluster. When I run the following query on hg18: select clusterID,name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd from knownIsoforms, knownGene where transcript = name; These are the results I get: | clusterID | name | chrom | strand | txStart | txEnd | cdsStart | cdsEnd | +-----------+------------+-------+--------+---------+--------+----------+--- -----+ | 1 | uc001aaa.1 | chr1 | + | 1736 | 4121 | 1736 | 1736 | | 2 | uc001aab.1 | chr1 | - | 4558 | 14764 | 4558 | 4558 | | 2 | uc001aac.1 | chr1 | - | 4558 | 19346 | 4558 | 4558 | | 2 | uc001aad.1 | chr1 | - | 4558 | 7231 | 4558 | 7173 | | 2 | uc001aae.1 | chr1 | - | 4558 | 9622 | 4558 | 4558 | | 2 | uc001aaf.1 | chr1 | - | 4832 | 19672 | 4832 | 4832 | | 2 | uc001aag.1 | chr1 | - | 5658 | 7231 | 5658 | 5658 | | 2 | uc001aah.1 | chr1 | - | 6720 | 19346 | 6720 | 6720 | | 2 | uc001aai.1 | chr1 | - | 6720 | 9622 | 6720 | 6720 | | 3 | uc001aaj.1 | chr1 | - | 7777 | 19346 | 7777 | 14749 | Shouldn't cluster 3 be included as part of cluster 4? Thank You, Jeffrey Rosenfeld _______________________________________________ Genome maillist - Genome at soe.ucsc.edu http://www.soe.ucsc.edu/mailman/listinfo/genome From archanat at soe.ucsc.edu Mon May 7 12:08:46 2007 From: archanat at soe.ucsc.edu (Archana Thakkapallayil) Date: Mon, 07 May 2007 12:08:46 -0700 Subject: [Genome] memory leaks in cartCheckout In-Reply-To: References: Message-ID: <463F793E.4020906@soe.ucsc.edu> Hello Adam, Thanks very much for pointing this out. We agree that this is not something important enough to worry about now. Fixing it could cause side effect problems. However, we would be interested to fix this issue in the future. Regards, Archana UCSC Genome Bioinformatics Group Adam Wenocur wrote: > Hi all, > > I was recently poking around the heap of the genome browser CGI > executables, and I noticed some peculiarities. > > Upon further inspection, I found that the cartCheckout function in > kent/src/hg/lib/cart.c is the source of some memory leaks: > > Instead of calling freeHash, cartCheckout should call > freeHashAndVals, since the values loaded into the cart are cloned > strings, and are otherwise orphaned. > There is the possibility that this solution might break the use of > cart parameter strings that were not copied prior to checking out the > cart, however it seems not to have caused any ill effect on my genome > browser mirror. > > A second issue doesn't appear to be causing leaks, but may have the > potential to: cartCheckout should use cartDbFreeList instead > cartDbFree, since userInfo and sessionInfo are indirectly assigned by > cartDbLoadWhere in cartNew, and could point to linked lists. > > I'm aware that this isn't of great importance to the CGI binaries, > since cartCheckout is usually called shortly before a program exits, > but I figure it couldn't hurt to note my observations. > > -Adam > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome > From dmitriy.skvortsov at gmail.com Mon May 7 12:45:03 2007 From: dmitriy.skvortsov at gmail.com (Dmitriy Skvortsov) Date: Mon, 7 May 2007 12:45:03 -0700 Subject: [Genome] broken URL Message-ID: <1acef0180705071245i356b55c0hac85afbbe957e8b2@mail.gmail.com> Dear colleagues , On page http://genome.ucsc.edu/goldenPath/customTracks/custTracks.html under Displaying Your Own Annotations in the Genome Browser we have URL http://genome.ucsc.edu/goldenPath/goldenPath/help/customTrack.html which does not work I believe that it should be replaced on http://genome.ucsc.edu/goldenPath/help/customTrack.html Thanks From donnak at soe.ucsc.edu Mon May 7 13:02:46 2007 From: donnak at soe.ucsc.edu (Donna Karolchik) Date: Mon, 7 May 2007 13:02:46 -0700 Subject: [Genome] broken URL References: <1acef0180705071245i356b55c0hac85afbbe957e8b2@mail.gmail.com> Message-ID: <029a01c790e2$b215cbd0$0ba8a8c0@donnakLT> hi Dmitriy, Thanks for reporting this -- we will fix it. -Donna ----------------------------------- Donna Karolchik UCSC Genome Bioinformatics Group http://genome.ucsc.edu ----- Original Message ----- From: "Dmitriy Skvortsov" To: Sent: Monday, May 07, 2007 12:45 PM Subject: [Genome] broken URL > Dear colleagues , > On page > http://genome.ucsc.edu/goldenPath/customTracks/custTracks.html > > under Displaying Your Own Annotations in the Genome Browser > we have URL > http://genome.ucsc.edu/goldenPath/goldenPath/help/customTrack.html > which does not work > > > I believe that it should be replaced on > http://genome.ucsc.edu/goldenPath/help/customTrack.html > Thanks > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome > From archanat at soe.ucsc.edu Mon May 7 13:29:56 2007 From: archanat at soe.ucsc.edu (Archana Thakkapallayil) Date: Mon, 07 May 2007 13:29:56 -0700 Subject: [Genome] knownIsoforms In-Reply-To: References: Message-ID: <463F8C44.4080500@soe.ucsc.edu> Hello Jeff, I would like to add this to Fan's reply: The clustering is done one strand at a time, and is done at the exon level. There are a few cases where you can have two transcripts that overlap before splicing, but don't overlap after splicing. The clustering is done in effect after splicing. I hope this information is helpful to you. If you have further questions please don't hesitate to contact us again. Regards, Archana UCSC Genome Bioinformatics Group Fan Hsu wrote: > Hi Jeff, > > The knownisoforms table is generated by a program txGeneCanonical, > written by Jim Kent. Jim is out of town today, not sure he has email access > or not. > > My guess is that this program first identifies overlapping genes and then > find the longest one and designate it as the representative > canonical gene of the cluster. > > In the mean time, you can find the details of this program > by downloading our src tree and find this program > under: > > kent/src/hg/txGene/txGeneCanonical > > Fan. > -----Original Message----- > From: genome-bounces at soe.ucsc.edu [mailto:genome-bounces at soe.ucsc.edu]On > Behalf Of Jeffrey Rosenfeld > Sent: Monday, May 07, 2007 10:16 AM > To: genome at soe.ucsc.edu > Subject: [Genome] knownIsoforms > > > How is the knownisoforms table constructed? It seems that all > overlapping genes are clustered together, but there are examples, such > as at the very beginning of chromosome 1, where a transcript within a > cluster becomes its own cluster. When I run the following query on hg18: > > select clusterID,name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd from > knownIsoforms, knownGene where transcript = name; > > These are the results I get: > > | clusterID | name | chrom | strand | txStart | txEnd | cdsStart > | cdsEnd | > +-----------+------------+-------+--------+---------+--------+----------+--- > -----+ > | 1 | uc001aaa.1 | chr1 | + | 1736 | 4121 | 1736 > | 1736 | > | 2 | uc001aab.1 | chr1 | - | 4558 | 14764 | 4558 > | 4558 | > | 2 | uc001aac.1 | chr1 | - | 4558 | 19346 | 4558 > | 4558 | > | 2 | uc001aad.1 | chr1 | - | 4558 | 7231 | 4558 > | 7173 | > | 2 | uc001aae.1 | chr1 | - | 4558 | 9622 | 4558 > | 4558 | > | 2 | uc001aaf.1 | chr1 | - | 4832 | 19672 | 4832 > | 4832 | > | 2 | uc001aag.1 | chr1 | - | 5658 | 7231 | 5658 > | 5658 | > | 2 | uc001aah.1 | chr1 | - | 6720 | 19346 | 6720 > | 6720 | > | 2 | uc001aai.1 | chr1 | - | 6720 | 9622 | 6720 > | 6720 | > | 3 | uc001aaj.1 | chr1 | - | 7777 | 19346 | 7777 > | 14749 | > > > Shouldn't cluster 3 be included as part of cluster 4? > > Thank You, > > Jeffrey Rosenfeld > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome > From morellr at nidcd.nih.gov Mon May 7 13:04:42 2007 From: morellr at nidcd.nih.gov (Morell, Robert (NIH/NIDCD) [E]) Date: Mon, 7 May 2007 16:04:42 -0400 Subject: [Genome] (no subject) Message-ID: <52C93A9A6058924E92A69CDF43966F1B01D86860@NIHCESMLBX8.nih.gov> I am having trouble with the DNA feature. The display does not annotate my custom tracks - only the standard UCSC tracks. The custom tracks are listed as line items on the Extended case/color options page, but selections have no effect on the subsequent DNA output page. Robert Morell, PhD Staff Scientist Laboratory of Molecular Genetics National Institute on Deafness and Other Communication Disorders (NIDCD) National Institutes of Health (NIH) 5 Research Ct. Rockville, MD 20850 301-402-4249 From archanat at soe.ucsc.edu Mon May 7 16:00:42 2007 From: archanat at soe.ucsc.edu (Archana Thakkapallayil) Date: Mon, 07 May 2007 16:00:42 -0700 Subject: [Genome] Chimp assembly 2 pairwise alignments In-Reply-To: <463F58BC.8050306@mcgill.ca> References: <463F58BC.8050306@mcgill.ca> Message-ID: <463FAF9A.6060009@soe.ucsc.edu> Hello Dan, Here is the response from one of our engineers: I think that the easiest way to do this is using Galaxy 2. This method will involve using the pairwise alignments extracted from the multiz multiple alignment (from the Conservation track). This is a best in genome alignment with the best aligning region for chimp aligned to each region of the human genome. This means that there is less information than in the chain track which contains all alignments (passing certain criteria) of the chimp genome to each region of the human genome. If this is ok, then you can use Galaxy by going to: http://test.g2.bx.psu.edu/ You will need to use the test version of Galaxy because this has the option of using our genome-test server. There are only panTro1 alignments in the 17-way alignment on hg18, but there are panTro2 alignments in the 28-way on hg18. Be aware that this our test server and that some of the data here (including the 28-way alignment) has not gone through our rigorous quality assurance checks. Here are the instructions to follow: 1) Go to http://test.g2.bx.psu.edu/ 2) Click on "Get Data" in the pane at the left side. 3) Click on "UCSC Test table browser" link in the expanded list. 4) In the middle an interface will appear that looks like the Table Browser. You can then select the Human Mar 2006 (hg18) assembly. Select Comparative Genomics as the group, 28-way Cons as the track and "multiz28wayAnno" as the table. Make sure that genome is selected as the region. Then select MAF as the output type. 5) Check the box that says "Send output to Galaxy". Press "get output" button and the "Send query to Galaxy" button. (Up to this point can also be done in the Table Browser on genome-test). Getting the MAF output seems to be rather slow. 6) Then from the "Get Data" menu, select "Upload File" and you can paste in or upload a file of the regions for which you want alignments (position or BED format is fine). 7) Then click on the "Fetch Sequences and Alignments" in the left pane. From the expanded list, select "Extract MAF blocks". First select the genomic intervals (query 2) and then press "Next Step" and select the MAF format output (query 1). The result is the multiple alignments for the regions defined by the user. 8) To limit this to only the pairwise alignment between human and chimp, select the "Maf Limit to Species" from the left pane and choose hg18 and panTro2. If you have questions about using Galaxy, you can contact their help desk: galaxy-user at bx.psu.edu If you would rather use the human/chimp chain or net alignments to get alignments for specific regions of the human genome, then we can walk you through using several of the programs that we have available for command line use in order to extract human/chimp pairwise alignments from this data. I hope this information is helpful to you. Let us know if you have further questions. Regards, Archana UCSC genome Bioinformatics Group Daniel Gaffney wrote: > Hi there, > I have ~ 1500 small regions in the human genome, for which I would like > to get the human-chimp > pairwise alignment for the latest chimp assembly. However, I'm having a > little trouble in figuring out the best > way to do this - can this be done locally? Or is there a batch > submission tool that I can retrieve all alignments > from UCSC directly - I've tried the table browser, but I can't seem to > get the specific region I want (i.e. if i select the chimp chain > track, and retrieve sequence, I get the the alignment of that entire > region, not just the region corresponding to the coordinates I've > entered). Any ideas? > Cheers > Dan > > From Xianjun.Dong at bccs.uib.no Tue May 8 05:37:27 2007 From: Xianjun.Dong at bccs.uib.no (Dong Xianjun) Date: Tue, 08 May 2007 14:37:27 +0200 Subject: [Genome] chain tracks by chromosome / strand In-Reply-To: References: <46276561.9070507@ii.uib.no> Message-ID: <46406F07.9090608@ii.uib.no> Hi, Rachel Thanks for your kind reply! Before I get into the source code, I prefer to ask for some possible options: --Do you have PSL files to download for the chain track? --otherwise, do you have script to convert the database table(those in "Annotation database") to PSL files? (I am guessing that could be the way how UCSC did in order to show the chain data) If yes for any of the above questions, I think I may save much time to create the track files for each chromosome (which could be a quick solution to split the data by chromosome.) Thanks for help Xianjun Rachel Harte wrote: > Hello Xianjun Dong, > > We do not have any plans to change the display of this track in this way. > If you would like to try it out yourself, you could set up a local version > of the Genome Browser and then you can change the display code as you > wish. The Genome Browser source code is free for academic, non-profit and > personal use. Here is information on dowloading the source code and > creating a local installation: > > http://genome.ucsc.edu/FAQ/FAQlicense > > See the FAQs on "Downloading the Genome Browser source" and "Mirroring the > Genome Browser". > > The chain files are in PSL format in the tables and may be downloaded from > our downloads server: http://hgdownload.cse.ucsc.edu/downloads.html > > If you follow the link to the appropriate organism and then click on the > "Annotation database" link there are downloadable files of the database > table definitions and the data for each table e.g. chrN_chainMm8 and > chrN_chainMm8Link files contain the data for the mouse mm8 chain tables. > These chain tables are split up so that there is one for each chromosome. > > I hope that this helps you. Please let us know if you have further > questions. We have a separate mailing list (genome-mirror at soe.ucsc.edu) > for questions regarding mirror setup. > > Rachel > > Rachel Harte > UCSC Genome Bioinformatics Group > http://genome.ucsc.edu > > > On Thu, 19 Apr 2007, Dong Xianjun wrote: > > >> Hi, >> >> I am thinking whether you could offer the chain track divided by >> chromosome and strand, for example, the chain on the same chr and same >> trand would be put in same row, each row presents chains on different >> chr/strand. Like, >> >> chr1(+): ========== ========-----========= =====---=====------------ >> chr2(-): ----------=====----------- >> -------------=========----- >> chr3(+): ---------======== ---------- >> ====== -------- >> chr4(+): >> chr4(-): ----------=====----------- ========= >> -----=========----- >> ...... >> >> This would make the chain looks more readable than either of the current >> display mode. >> >> Just one opinion, esp. when I felt tired of reading the genome data for >> a whole day. Sure, it could bring more work. >> >> If you could offer the download link for the chains.bed file, I may be >> able to do it by myself. >> >> Thanks >> >> -- >> --------------------------- >> Sterding (Xianjun) Dong >> PhD student, Boris Lenhard's group >> Bergen Center of Computational Science >> Bergen University, Norway >> Mobile: 0047-47361688 >> Telephone: 0047-55276381 >> Skype: xianjun.dong >> >> _______________________________________________ >> Genome maillist - Genome at soe.ucsc.edu >> http://www.soe.ucsc.edu/mailman/listinfo/genome >> >> -- --------------------------- Sterding (Xianjun) Dong PhD student, Boris Lenhard's group Bergen Center of Computational Science Bergen University, Norway Mobile: 0047-47361688 Telephone: 0047-55276381 Skype: xianjun.dong From archanat at soe.ucsc.edu Tue May 8 09:50:51 2007 From: archanat at soe.ucsc.edu (Archana Thakkapallayil) Date: Tue, 08 May 2007 09:50:51 -0700 Subject: [Genome] (no subject) In-Reply-To: <52C93A9A6058924E92A69CDF43966F1B01D86860@NIHCESMLBX8.nih.gov> References: <52C93A9A6058924E92A69CDF43966F1B01D86860@NIHCESMLBX8.nih.gov> Message-ID: <4640AA6B.7060704@soe.ucsc.edu> Hello Robert, Thanks for pointing this out. Our developers will be looking into fixing this issue. I will let you know when it is fixed. Regards, Archana UCSC Genome Bioinformatics Group Morell, Robert (NIH/NIDCD) [E] wrote: > I am having trouble with the DNA feature. The display does not annotate > my custom tracks - only the standard UCSC tracks. The custom tracks are > listed as line items on the Extended case/color options page, but > selections have no effect on the subsequent DNA output page. > > > > Robert Morell, PhD > > Staff Scientist > > Laboratory of Molecular Genetics > > National Institute on Deafness and Other Communication Disorders (NIDCD) > > National Institutes of Health (NIH) > > > > 5 Research Ct. > > Rockville, MD 20850 > > > > 301-402-4249 > > > > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome > From scai at lbl.gov Tue May 8 10:57:37 2007 From: scai at lbl.gov (Shutao) Date: Tue, 8 May 2007 10:57:37 -0700 Subject: [Genome] BLAT search Inquiry Message-ID: <9B5E0D4E-FD8D-11DB-B28F-000393AAD89C@lbl.gov> Dear Sir/Madam, I have a large batch queries need to be performed for academic research. I am wondering what is efficient ways to access your data. The following is the message I received from your BLAT search site. "There is a very high volume of traffic coming from your site (IP address 131.243.59.247) as of Tue May 8 10:45:41 2007 (California time). So that other users get a fair share of our bandwidth, we are putting in a delay of 10.1 seconds before we service your request. This delay will slowly decrease over a half hour as activity returns to normal. This high volume of traffic is likely due to program-driven rather than interactive access, or the submission of queries on a large number of sequences. If you are making large batch queries, please write to our genome at cse.ucsc.edu public mailing list and inquire about more efficient ways to access our data. If you are sharing an IP address with someone who is sumitting large batch queries, we apologize for the inconvenience. Please contact genome-www at cse.ucsc.edu if you think this delay is being imposed unfairly." Thank you very much for your assistance. Shutao Cai Life Sciences Division Lawrence Berkeley Laboratory University of California Berkeley, CA 94720 From yueming.ding at jax.org Tue May 8 10:34:08 2007 From: yueming.ding at jax.org (Yueming Ding) Date: Tue, 8 May 2007 13:34:08 -0400 Subject: [Genome] blat Message-ID: <20070508133408126.00000000676@sable> Generator Microsoft Word 11 (filtered medium) Hi, is anyone able to tell me how Jim' s BLAT handles mismatch and indels? Does BLAT treat mismatch and indels equally (by assigning the same penalty scores)? Thanks. Yueming Ding The Jackson Laboratory From hongyu at relativegenetics.com Tue May 8 11:46:38 2007 From: hongyu at relativegenetics.com (hongyu@relativegenetics.com) Date: Tue, 8 May 2007 12:46:38 -0600 Subject: [Genome] (no subject) Message-ID: <722DC6DFD1F97C4098207F71F0244293E33A2B@hera.SDIHQ.com> I am a R&D technologist from Sorenson Genomics, LLC. I have noticed your web site was updated lately therefore some our primer sets are not found in your web set as used to be. Any help would be appreciated. Thanks Hongyu From goshng at gmail.com Tue May 8 12:54:19 2007 From: goshng at gmail.com (Sang Chul Choi) Date: Tue, 8 May 2007 15:54:19 -0400 Subject: [Genome] Encode and dbSNP Message-ID: <33f36270705081254p5ce49821tfb4e14a9cbb530d6@mail.gmail.com> Hi, I have a question about ENCODE data in the genome browser. I want to get SNPs with dbSNP rsID only generated by ENCODE project. Is there any Table for this in UCSC genome browser? Thank you, Sang Chul -- =============================== Live, Learn, and Love! E-mail : goshng at empal dot com goshng at gmail dot com =============================== From kayla at soe.ucsc.edu Tue May 8 13:27:05 2007 From: kayla at soe.ucsc.edu (Kayla Smith) Date: Tue, 08 May 2007 13:27:05 -0700 Subject: [Genome] BLAT search Inquiry In-Reply-To: <9B5E0D4E-FD8D-11DB-B28F-000393AAD89C@lbl.gov> References: <9B5E0D4E-FD8D-11DB-B28F-000393AAD89C@lbl.gov> Message-ID: <4640DD19.6060901@cse.ucsc.edu> Shutao, Here is a link to our BLAT use restrictions: http://genome.ucsc.edu/FAQ/FAQblat.html#blat2 The block on your IP decays slowly over time, and it your IP address appears to be clear now. Here is a previously answered mailing question which you may find useful: https://www.soe.ucsc.edu/pipermail/genome/2007-April/013388.html I hope this information is helpful to you. Please don't hesitate to contact us again if you require further assistance. Kayla Smith UCSC Genome Bioinformatics Group Shutao wrote: > Dear Sir/Madam, > > I have a large batch queries need to be performed for academic > research. I am wondering what is efficient ways to access your data. > The following is the message I received from your BLAT search site. > > "There is a very high volume of traffic coming from your site (IP > address 131.243.59.247) as of Tue May 8 10:45:41 2007 (California > time). So that other users get a fair share of our bandwidth, we are > putting in a delay of 10.1 seconds before we service your request. This > delay will slowly decrease over a half hour as activity returns to > normal. This high volume of traffic is likely due to program-driven > rather than interactive access, or the submission of queries on a large > number of sequences. If you are making large batch queries, please > write to our genome at cse.ucsc.edu public mailing list and inquire about > more efficient ways to access our data. If you are sharing an IP > address with someone who is sumitting large batch queries, we apologize > for the inconvenience. Please contact genome-www at cse.ucsc.edu if you > think this delay is being imposed unfairly." > > > Thank you very much for your assistance. > > > Shutao Cai > Life Sciences Division > Lawrence Berkeley Laboratory > University of California > Berkeley, CA 94720 > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome From kayla at soe.ucsc.edu Tue May 8 14:13:05 2007 From: kayla at soe.ucsc.edu (Kayla Smith) Date: Tue, 08 May 2007 14:13:05 -0700 Subject: [Genome] Encode and dbSNP In-Reply-To: <33f36270705081254p5ce49821tfb4e14a9cbb530d6@mail.gmail.com> References: <33f36270705081254p5ce49821tfb4e14a9cbb530d6@mail.gmail.com> Message-ID: <4640E7E1.5090902@cse.ucsc.edu> Sang Chul, On the human (hg17) assembly there is a track called "HapMap SNPs". It is in the "ENCODE Variation" section. This is a composite track, with 4 tables that look like "encodeHapMapAlleleFreq%", where % is {CEU, CHB, JPT, YRI}. These tables are available for download from http://hgdownload.cse.ucsc.edu/goldenPath/hg17/database/ I hope this data is helpful to you. Please don't hesitate to contact us again if you require further assistance. Kayla Smith UCSC Genome Bioinformatic Group Sang Chul Choi wrote: > Hi, > > I have a question about ENCODE data in the genome browser. I want to > get SNPs with dbSNP rsID only generated by ENCODE project. Is there > any Table for this in UCSC genome browser? > > Thank you, > > Sang Chul > From kayla at soe.ucsc.edu Tue May 8 14:16:18 2007 From: kayla at soe.ucsc.edu (Kayla Smith) Date: Tue, 08 May 2007 14:16:18 -0700 Subject: [Genome] blat In-Reply-To: <20070508133408126.00000000676@sable> References: <20070508133408126.00000000676@sable> Message-ID: <4640E8A2.8090807@cse.ucsc.edu> Yueming, I've asked one of our developers about your question and here is what he has to say: Please see "Replicating web-based Blat percent identity and score calculations" http://genome.ucsc.edu/FAQ/FAQblat.html#blat4 which has all details needed to calculate our hgBlat score. Indels and mismatches are not treated the same, that includes how BLAT does alignments and how it calculates the final score. BLAT builds the exons as alignments with matches/mismatches extending from the seed position until the alignment cannot be extended. Then the parts are chained together giving a final alignment that has exons and introns. All the details of the score calculation are given above. In general huge introns do not carry a huge penalty. It's not subtracting one for each base of the intron gap. It actually only subtracts one for the entire gap or insert. In general also a mismatch consumes a base from the query side whereas a gap does not, e.g. mismatch T/C (T in query is consumed) query: ACTGACTG target: ACCGACTG gap example (gap on query side, nothing in query is consumed) query: ACT---------GACTG target: ACTCGCCGGCCCGACTG Note on repeatMatches: Despite the documentation, the repeatMatches feature of the psls is basically not used, so you won't see anything in that column. Instead, a match in a repeated area will just be a regular match. I hope this information is helpful to you. Please don't hesitate to contact us again if you require further assistance. Kayla Smith UCSC Genome Bioinformatics Group Yueming Ding wrote: > Generator Microsoft Word 11 (filtered medium) Hi, is anyone able to tell me how Jim' s BLAT handles mismatch and indels? Does BLAT treat mismatch and indels equally (by assigning the same penalty scores)? Thanks. > > Yueming Ding > The Jackson Laboratory > _______________________________________________ > Genome maillist - Genome at soe.ucsc.edu > http://www.soe.ucsc.edu/mailman/listinfo/genome > From - Tue From bnelson at burnham.org Tue May 8 15:31:39 2007 From: bnelson at burnham.org (Brandon) Date: Tue, 8 May 2007 15:31:39 -0700 Subject: [Genome] 3' UTR help.... Message-ID: <000001c791c0$a5605250$9efb10ac@gatewaym58xnn8> Hello all, I am new to this site and I was inquiring if I could get some help with a couple questions.. 1. I have the list of all the Human 3'UTR's from your database and I would like to Blast them to find certain sequences. 2. With the hits from 1, I would like to expand the 3' utr ~70 bp 5' & 3' and upload to mFold, or some other similar program, to determine delta-g for those sequences. Any advice as to how I could accomplish this would be greatly appreciated. Thanks in advance for your time. Brandon From plibrado at ub.edu Wed May 9 02:41:28 2007 From: plibrado at ub.edu (Pablo Librado) Date: Wed, 09 May 2007 11:41:28 +0200 Subject: [Genome] UCSC through DnaSP? Message-ID: <46419748.7050703@ub.edu> Hi all, My name is Pablo. I' m a student of Barcelona University and I' m developing new features in DnaSP (http://www.ub.edu/dnasp) software. One of these makes possible to the users the search of their sequences in UCSC through BLAT or through a search of a term. Also is possible to visualize the standard tracks of the sequence positions together with sliding-windows (custom tracks) of some evolutionary statistics. All of these is done through a DnaSP browser. I' m afraid about the maintenance and stability of the Web. I need to know if the next elements are stables (because I interpret them in the DnaSP code): -I use these URLs: http://genome.ucsc.edu/cgi-bin/hgCustom http://genome.ucsc.edu/cgi-bin/hgGateway http://genome.ucsc.edu/cgi-bin/hgTracks http://genome.ucsc.edu/cgi-bin/hgBlat http://genome.ucsc.edu/cgi-bin/cartReset -These web elements and their attributes: in the main (genome browser) URL (http://genome.ucsc.edu/cgi-bin/hgGateway) I use the name="org" attribute and that it is a combo element (SELECT in HTML) I use the name="position" attr