[Genome] question about ucsc browser

Rachel Harte hartera at soe.ucsc.edu
Tue Dec 12 13:56:15 PST 2006 

Hello Zhaodong,

Thank you for reporting this problem We have been able to reproduce it.
The tracks appear to load and display, but it fails after loading - hitting
the Manage button causes the display of the error message that you saw.

One of our developers is working to fix this problem now. I will let you
know when it is fixed.

Rachel

Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


> ----- Original Message -----
> From: "Zhaodong Xu" <zxu at uhnres.utoronto.ca>
> To: "Donna Karolchik" <donnak at soe.ucsc.edu>
> Sent: Tuesday, December 12, 2006 7:16 AM
> Subject: question about ucsc browser
>
>
> > hi donna,
> >
> > I have a question to bother you, we set up a custom track using your
> > browser, it works just fine before.  today one collague came over saying
> > that he cannot access the custom track, there is error coming out. I
> > checked it, it did have some error, the message is
> > ____________________________________________________
> > Unmatched '
> > ____________________________________
> > line1 of input:missing closing'
> >
> > ______________________________
> >
> > our web address is:
> > http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm6&position=chr10&hgt.customText=http://vsrp.uhnres.utoronto.ca/mousearray.gff
> >
> > do you know what kind of problem it is? it is working before, I thought
> > it might be some setting problem?
> >
> >
> > Thanks
> >
> > Zhaodong
> > TWRI
> >
> >
> > Donna Karolchik wrote:
> >>
> >> Zhaodong,
> >>
> >> The motif is occurring on the minus strand. To find it in the Genome
> >> Browser, you either need to reverse complement the motif sequence or look
> >> for the motif sequence on a reverse-complemented version of the genome
> >> sequence (you can view this via the DNA link in the top menu bar on the
> >> browser). In the example you give for AB025922 below, I found the reverse
> >> motif sequence (TGGGTGGTC) at chr10:130,609,705-130,609,713.
> >>
> >> -Donna
> >>
> >> ----- Original Message -----
> >> From: "Zhaodong Xu" <zxu at uhnres.utoronto.ca>
> >> To: "Donna Karolchik" <donnak at soe.ucsc.edu>
> >> Sent: Tuesday, March 30, 2004 8:05 AM
> >> Subject: Re: [Genome] question about ucsc browser
> >>
> >> > thanks Donna,
> >> >
> >> > you are really helpful, but I still have the question, for exampl, for
> >> > #1, this time, I don't pad the 5000 upstream and downstream, I down the
> >> > file, it is in the right coordinate,
> >> >  >mm4_mrna_AB025922 range=chr10:130608159-130616522 5'pad=0 3'pad=0
> >> > revComp=TRUE strand=- repeatMasking=N
> >> >
> >> > this time, I don't use the program, I just use find function in word,
> >> > looking for GACCACCCA, it will be find in line 138, position:10, which
> >> > is about 6810 base from the first base of this seq, so the starting
> >> > position of GACCACCCA should be 130608159 + 6810 = 130,614,968.  but I
> >> > cannot find it in ucsc genome browser, I copy the 50 bases seq around
> >> > the GACCACCCA, and blat it, I found it position at 130,609,705-
> >> > 130,609,722.
> >> >
> >> > could you tell me the reason for that?
> >> >
> >> > thanks very much
> >> >
> >> > zhaodong
> >> >
> >> > Donna Karolchik wrote:
> >> > >
> >> > > OK, now I see what you're doing. The positions of your mRNA downloads
> >> differ
> >> > > from those in the Genome Browser because you are padding your mRNAs by
> >> 5000
> >> > > bases on each side. That is why your position for X60664 starts at
> >> 61375183.
> >> > > The mRNA sequence actually starts at 61380183, but you have added 5000
> >> bases
> >> > > to the beginning of it, which changes it to 61375183. This is why you
> >> are
> >> > > not able to find some of your motif hits...they fall in the 5000-base
> >> > > upstream/downstream region rather than in the actual mRNA sequence.
> >> > >
> >> > > For example, in #1 below, the actual mRNA sequence range for AB025922 is
> >> > > chr10:130608159-130616522. With the 5000-base padding on either side, it
> >> > > becomes chr10:130603159-130621522. Your motif falls at 130617370, which
> >> is
> >> > > within the padded range, but is outside the actual mRNA sequence range.
> >> > >
> >> > > -Donna
> >> > >
> >> > > ----- Original Message -----
> >> > > From: "Zhaodong Xu" <zxu at uhnres.utoronto.ca>
> >> > > To: "Donna Karolchik" <donnak at soe.ucsc.edu>
> >> > > Sent: Monday, March 29, 2004 10:44 AM
> >> > > Subject: Re: [Genome] question about ucsc browser
> >> > >
> >> > > > thanks for your reply, the coordinates for x60664 in my input file are
> >> > > > chr18:61375183-61453417, which is different from yours, chr18:
> >> > > > 61380183-61448417, according to your email, I donot have the latest
> >> > > > file, but the file I got is just from your genome browser, I don't
> >> think
> >> > > > it is the program problem, it is due to original file coordinate is
> >> > > > different to yours, since in the previou #1, #3, sequence, I check the
> >> > > > differnece between is the same as you find out in the genome brwoser
> >> > > > between #1, #3.
> >> > > >
> >> > > > But the question is I got the seq from your browser, here is How I get
> >> > > > the X60664 seq, if you follow it, you will get the same coordinate as
> >> > > > mine, in ucsc genome table browser, Mouse oct 2003, chooose Mouse
> >> mRNAs
> >> > > > talbe, select Item, paste in Names/Accessions, past X60664, submit,
> >> then
> >> > > > get sequence...,
> >> > > > in the sequence Retrieval regions options:
> >> > > > select Promoter/Upstream by 5000 bases, select blocks, select regions
> >> > > > between blcoks, select downstream by 5000 bases, select one FASTA
> >> record
> >> > > > per item,
> >> > > > in sequence formatting options
> >> > > > select All upper case
> >> > > > select Mask repeats: to N
> >> > > >
> >> > > > then push Get sequence button
> >> > > >
> >> > > > I get :
> >> > > >
> >> > > > >mm4_mrna_X60664 range=chr18:61375183-61453417 5'pad=0 3'pad=0
> >> > > revComp=FALSE strand=+ repeatMasking=N
> >> > > >
> >> > > > I don't know how do you get chr18:61380183-61448417?  the program I
> >> used
> >> > > > is based on the input files >mm4_mrna_X60664
> >> > > > range=chr18:61375183-61453417 5'pad=0 3'pad=0 revComp=FALSE strand=+
> >> > > > repeatMasking=N, if the input coordinates is different, then the motif
> >> > > > are of course shifted.
> >> > > >
> >> > > >
> >> > > >
> >> > > >
> >> > > >
> >> > > > zhaodong
> >> > > >
> >> > > >
> >> > > > Donna Karolchik wrote:
> >> > > > >
> >> > > > > I just double-checked the data points below between the Genome
> >> Browser
> >> > > and
> >> > > > > our mRNA downloads file, and the UCSC data is in synch. For example,
> >> the
> >> > > > > coordinates for X60664 are listed as chr18:61380183-61448417 in both
> >> the
> >> > > > > Browser and the downloads file for chr18_mrna.
> >> > > > >
> >> > > > > It sounds like the program you are using is generating incorrect
> >> > > positions.
> >> > > > > You could easily determine this by examining the input coordinates
> >> and
> >> > > > > comparing them with the output coordinates. For example, the
> >> coordinates
> >> > > for
> >> > > > > X60664 in your input file should match those I've listed above. If
> >> they
> >> > > > > don't, you don't have the latest file from us. Similarly, the output
> >> > > > > coordinates for the corresponding motif should fall somewhere within
> >> the
> >> > > > > chr18:61380183-61448417 range. If they don't, the program is
> >> generating
> >> > > > > incorrect positions.
> >> > > > >
> >> > > > > If your program is consistently shifting the data positions by the
> >> same
> >> > > > > amount, perhaps you can compensate for it in your results?
> >> > > > >
> >> > > > > Hope this helps...
> >> > > > >
> >> > > > > -Donna
> >> > > > >
> >> > > > > ----- Original Message -----
> >> > > > > From: "Zhaodong Xu" ?zxu at uhnres.utoronto.ca?
> >> > > > > To: "Donna Karolchik" ?donnak at soe.ucsc.edu?
> >> > > > > Sent: Friday, March 26, 2004 7:50 AM
> >> > > > > Subject: Re: [Genome] question about ucsc browser
> >> > > > >
> >> > > > > ? hi, Donna,
> >> > > > > ?
> >> > > > > ? thanks for your reply, from your response, if I compare the
> >> distance
> >> > > > > ? between 3, and 1 since they are in the same chr, I can get they
> >> are
> >> > > > > ? separate by 2402 base,(130609705-130607303), then I did same thing
> >> by
> >> > > my
> >> > > > > ? program, which is also 2402, (130617370-130614968), so obviously
> >> the
> >> > > > > ? coordinate are shifted. I just download a new file, and run the
> >> > > program,
> >> > > > > ? also it was shifted, I don't know why, maybe mrna and genome
> >> browser
> >> > > > > ? don't quite match?
> >> > > > > ?
> >> > > > > ? zhaodong
> >> > > > > ?
> >> > > > > ? Donna Karolchik wrote:
> >> > > > > ? ?
> >> > > > > ? ? Zhaodong,
> >> > > > > ? ?
> >> > > > > ? ? It looks like the data in your file Gli.faa.txt does not match
> >> the
> >> > > data
> >> > > > > in
> >> > > > > ? ? the mm4 Genome Browser. For example, in your file the position
> >> of
> >> > > X60664
> >> > > > > is
> >> > > > > ? ? listed as chr18:61375183-61453417, but in the Genome Browser
> >> it's
> >> > > found
> >> > > > > at
> >> > > > > ? ? chr18:61380183-61448417. I found similar differences with other
> >> > > mRNAs in
> >> > > > > ? ? your file. FYI, the GenBank data in the Genome Browser is
> >> updated
> >> > > > > nightly
> >> > > > > ? ? from GenBank...my guess is that you're using data that's
> >> slightly
> >> > > out of
> >> > > > > ? ? date.
> >> > > > > ? ?
> >> > > > > ? ? FYI, I did find find hits for your motifs in #1 ? 3 in the mm4
> >> > > Genome
> >> > > > > ? ? Browser. Both of these were found on the reverse strand. Here
> >> they
> >> > > are:
> >> > > > > ? ?
> >> > > > > ? ? 1. ?mm4_dna range=chr10:130607303-130607311 5'pad=0 3'pad=0
> >> > > revComp=TRUE
> >> > > > > ? ? strand=? repeatMasking=none
> >> > > > > ? ? GAACACCCA
> >> > > > > ? ?
> >> > > > > ? ? 3. ?mm4_dna range=chr10:130609705-130609713 5'pad=0 3'pad=0
> >> > > revComp=TRUE
> >> > > > > ? ? strand=? repeatMasking=none
> >> > > > > ? ? GACCACCCA
> >> > > > > ? ?
> >> > > > > ? ? To find these, I brought up the chromosome positions from
> >> gliFaa.txt
> >> > > for
> >> > > > > the
> >> > > > > ? ? mRNAs where you found the motif hits in the Genome Browser, then
> >> > > clicked
> >> > > > > the
> >> > > > > ? ? DNA link in the top menu bar. On the Get DNA configuration page,
> >> I
> >> > > > > selected
> >> > > > > ? ? the reverse complement option, then clicked the Get DNA button.
> >> On
> >> > > the
> >> > > > > page
> >> > > > > ? ? that shows the sequence, I used my browser's Find option (I'm
> >> using
> >> > > IE,
> >> > > > > ? ? where it's located on the Edit menu) to search for the motif
> >> string
> >> > > > > within
> >> > > > > ? ? the sequence.
> >> > > > > ? ?
> >> > > > > ? ? I'd suggest you update your data and try again...hopefully
> >> you'll
> >> > > get
> >> > > > > ? ? results that better match the Genome Browser data.
> >> > > > > ? ?
> >> > > > > ? ? -Donna
> >> > > > > ? ?
> >> > > > > ? ? ----- Original Message -----
> >> > > > > ? ? From: "Zhaodong Xu" ?zxu at uhnres.utoronto.ca?
> >> > > > > ? ? To: "Donna Karolchik" ?donnak at soe.ucsc.edu?
> >> > > > > ? ? Sent: Thursday, March 25, 2004 1:58 PM
> >> > > > > ? ? Subject: Re: [Genome] question about ucsc browser
> >> > > > > ? ?
> >> > > > > ? ? ? ok, I attached 2 files, one file is gli.faa, and another is
> >> > > glimotif.
> >> > > > > so
> >> > > > > ? ? ? I run the program to check how many sequences in gli.faa
> >> contain
> >> > > > > ? ? ? glimotif.  the results are following:
> >> > > > > ? ? ?
> >> > > > > ? ? ? 1. Organism::Mouse; Motif::GAACACCCA;
> >> Chromosome::chr10:130603159;
> >> > > > > ? ? ? Position::130617370; Range::chr10:130617370-130617420
> >> > > > > ? ? ?
> >> > > > > ? ? ? 2. Organism::Mouse; Motif::GAACACCCA;
> >> Chromosome::chr18:61375183;
> >> > > > > ? ? ? Position::61398377; Range::chr18:61398377-61398427
> >> > > > > ? ? ?
> >> > > > > ? ? ? 3. Organism::Mouse; Motif::GACCACCCA;
> >> Chromosome::chr10:130603159;
> >> > > > > ? ? ? Position::130614968; Range::chr10:130614968-130615018
> >> > > > > ? ? ?
> >> > > > > ? ? ? for 2, it was just there if you paste chr18:61398377-61398427
> >> in
> >> > > > > genome
> >> > > > > ? ? ? browser, it shows GACCACCCA on reverse strand,
> >> > > > > ? ? ?
> >> > > > > ? ? ? but for 1, 3, I cannot find the motif GAACACCCA on either
> >> strand.
> >> > > > > ? ? ?
> >> > > > > ? ? ?
> >> > > > > ? ? ? thanks for your attention.
> >> > > > > ? ? ?
> >> > > > > ? ? ?
> >> > > > > ? ? ? zhaodong
> >> > > > > ? ? ?
> >> > > > > ? ? ?
> >> > > > > ? ? ? Donna Karolchik wrote:
> >> > > > > ? ? ? ?
> >> > > > > ? ? ? ? Can you give me a specific example of a case where the
> >> > > coordinates
> >> > > > > don't
> >> > > > > ? ? ? ? match? How are you determining the genome browser position
> >> of
> >> > > the
> >> > > > > ? ? motifs?
> >> > > > > ? ? ? ? Perhaps they are aligning in multiple places in the browser?
> >> > > Also,
> >> > > > > the
> >> > > > > ? ? ? ? genomic sequence has been repeat-masked - if you are using
> >> mRNA
> >> > > > > sequence
> >> > > > > ? ? ? ? that hasn't been masked, this could cause misalignments.
> >> > > > > ? ? ? ?
> >> > > > > ? ? ? ? -Donna
> >> > > > > ? ? ? ?
> >> > > > > ? ? ? ? ----- Original Message -----
> >> > > > > ? ? ? ? From: "Zhaodong Xu" ?zxu at uhnres.utoronto.ca?
> >> > > > > ? ? ? ? To: "Donna Karolchik" ?donnak at soe.ucsc.edu?
> >> > > > > ? ? ? ? Cc: ?zxu at uhnres.utoronto.ca?
> >> > > > > ? ? ? ? Sent: Thursday, March 25, 2004 1:38 PM
> >> > > > > ? ? ? ? Subject: Re: [Genome] question about ucsc browser
> >> > > > > ? ? ? ?
> >> > > > > ? ? ? ? ? thanks again for your help.
> >> > > > > ? ? ? ? ?
> >> > > > > ? ? ? ? ?
> >> > > > > ? ? ? ? ? the reason I am asking this question is that I downed big
> >> > > mouse
> >> > > > > mrna
> >> > > > > ? ? ? ? ? sequences from table browser using some access #, but I
> >> leave
> >> > > all
> >> > > > > the
> >> > > > > ? ? ? ? ? sequence in( without delete the repeat mask), then I run
> >> some
> >> > > > > program
> >> > > > > ? ? ? ? ? against some transcription factor bind sequences to find
> >> if
> >> > > these
> >> > > > > ? ? motif
> >> > > > > ? ? ? ? ? are in these sequences, from the program, I can get the
> >> motif
> >> > > > > position
> >> > > > > ? ? ? ? ? in some chromosome, then I put these position coordinates
> >> back
> >> > > in
> >> > > > > the
> >> > > > > ? ? ? ? ? genome browser, some motif are the exact position in the
> >> > > genome
> >> > > > > ? ? ? ? ? browser(I can see these seq in the genome browser since I
> >> only
> >> > > see
> >> > > > > 50
> >> > > > > ? ? ? ? ? base), but some motif are not in the position they should
> >> be.
> >> > > I
> >> > > > > am
> >> > > > > ? ? sure
> >> > > > > ? ? ? ? ? that the program find the right position, or else, all the
> >> > > > > position
> >> > > > > ? ? ? ? ? should be wrong, that's the reason I ask the question. it
> >> > > seems
> >> > > > > some
> >> > > > > ? ? ? ? ? mRNA position coordiantes not correspond to the genome
> >> browser
> >> > > > > postion
> >> > > > > ? ? ? ? ? coordinates.
> >> > > > > ? ? ? ? ?
> >> > > > > ? ? ? ? ? Donna Karolchik wrote:
> >> > > > > ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? Zhaodong,
> >> > > > > ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? The mRNA position coordinates correspond to the genome
> >> > > browser
> >> > > > > ? ? position
> >> > > > > ? ? ? ? ? ? coordinates. Because the mRNAs are alignments to the
> >> genomic
> >> > > > > ? ? sequence,
> >> > > > > ? ? ? ? they
> >> > > > > ? ? ? ? ? ? may differ somewhat from the actual genomic sequence.
> >> The
> >> > > mRNAs
> >> > > > > are
> >> > > > > ? ? ? ? aligned
> >> > > > > ? ? ? ? ? ? using the Blat program. Alignments must also have at
> >> least 9
> >> > > 5%
> >> > > > > base
> >> > > > > ? ? ? ? identity
> >> > > > > ? ? ? ? ? ? with the genomic sequence to be displayed, and only
> >> > > alignments
> >> > > > > that
> >> > > > > ? ? have
> >> > > > > ? ? ? ? a
> >> > > > > ? ? ? ? ? ? base identity level within 1% of the best alignment are
> >> > > kept.
> >> > > > > ? ? Therefore,
> >> > > > > ? ? ? ? you
> >> > > > > ? ? ? ? ? ? can expect some variation, but not a lot.
> >> > > > > ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? Please let us know if you find an alignment with more
> >> > > > > discrepancy
> >> > > > > ? ? than
> >> > > > > ? ? ? ? you'd
> >> > > > > ? ? ? ? ? ? expect, given the above parameters.
> >> > > > > ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? -Donna
> >> > > > > ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ----- Original Message -----
> >> > > > > ? ? ? ? ? ? From: "Zhaodong Xu" ?zxu at uhnres.utoronto.ca?
> >> > > > > ? ? ? ? ? ? To: "Donna Karolchik" ?donnak at soe.ucsc.edu?
> >> > > > > ? ? ? ? ? ? Sent: Thursday, March 25, 2004 7:02 AM
> >> > > > > ? ? ? ? ? ? Subject: Re: [Genome] question about ucsc browser
> >> > > > > ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? thanks for the reply, it really answers my question.
> >> > > > > ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? another question: I downed some sequence from table
> >> > > browser, a
> >> > > > > ? ? short
> >> > > > > ? ? ? ? ? ? ? sequence is here:
> >> > > > > ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? ?mm4_mrna_D49544 range=chr17:26542617-26568050 5'pad=0
> >> > > 3'pad=0
> >> > > > > ? ? ? ? ? ? revComp=FALSE strand=+ repeatMasking=none
> >> > > > > ? ? ? ? ? ? ? TCAAAGTGGAAGGAATCCCCACTTGGGTCCACGCATCCCACGTCAAGAGA
> >> > > > > ? ? ? ? ? ? ? GAACCCCCTGGAGTCAGCCATGATGAGTGGACTTTGGAGAAGACTACTAA
> >> > > > > ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? my question is: does it coordinate corresponded to
> >> genome
> >> > > > > browser
> >> > > > > ? ? ? ? since
> >> > > > > ? ? ? ? ? ? ? it is mrna sequence? my trial with this is sometimes
> >> it
> >> > > does,
> >> > > > > ? ? ? ? sometimes
> >> > > > > ? ? ? ? ? ? ? it does not.
> >> > > > > ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? zhaodong
> >> > > > > ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? Donna Karolchik wrote:
> >> > > > > ? ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? ? Hi,
> >> > > > > ? ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? ? You can find a list of all the Genome Browser
> >> assemblies
> >> > > and
> >> > > > > ? ? their
> >> > > > > ? ? ? ? ? ? internal
> >> > > > > ? ? ? ? ? ? ? ? database names (e.g. hg, mm, galGal) at
> >> > > > > ? ? ? ? ? ? ? ? http://genome.ucsc.edu/FAQ/FAQreleases#release1.
> >> > > > > ? ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? ? -Donna
> >> > > > > ? ? ? ? ? ? ? ? -----------------------------------
> >> > > > > ? ? ? ? ? ? ? ? Donna Karolchik
> >> > > > > ? ? ? ? ? ? ? ? UCSC Genome Bioinformatics Group
> >> > > > > ? ? ? ? ? ? ? ? donnak at soe.ucsc.edu
> >> > > > > ? ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? ? ----- Original Message -----
> >> > > > > ? ? ? ? ? ? ? ? From: "Vince Forgetta"
> >> ?vince.forgetta at staff.mcgill.ca?
> >> > > > > ? ? ? ? ? ? ? ? To: "Zhaodong Xu" ?zxu at uhnres.utoronto.ca?
> >> > > > > ? ? ? ? ? ? ? ? Cc: ?genome at soe.ucsc.edu?
> >> > > > > ? ? ? ? ? ? ? ? Sent: Tuesday, March 23, 2004 6:35 AM
> >> > > > > ? ? ? ? ? ? ? ? Subject: Re: [Genome] question about ucsc browser
> >> > > > > ? ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? ? ? The unique genome names can been seen at the top
> >> of
> >> > > each
> >> > > > > ? ? download
> >> > > > > ? ? ? ? link
> >> > > > > ? ? ? ? ? ? ? ? ? group on this page:
> >> > > > > ? ? ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? ? ? http://genome.ucsc.edu/downloads.html
> >> > > > > ? ? ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? ? ? Zhaodong Xu wrote:
> >> > > > > ? ? ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? ? ? ?hi, how are you doing?
> >> > > > > ? ? ? ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? ? ? ?my name is zhaodong xu, from toronto western
> >> > > hospital, I
> >> > > > > want
> >> > > > > ? ? to
> >> > > > > ? ? ? ? ? ? ? ? ? ?hyperlink  some program to your browser, I saw
> >> your
> >> > > FAQ
> >> > > > > about
> >> > > > > ? ? how
> >> > > > > ? ? ? ? to
> >> > > > > ? ? ? ? ? ? ? ? ? ?hyperlink. I have a question, how do I know if I
> >> > > download
> >> > > > > a
> >> > > > > ? ? ? ? sequence
> >> > > > > ? ? ? ? ? ? ? ? ? ?from your browser, it is from Chicken not from
> >> mouse
> >> > > or
> >> > > > > ? ? human,
> >> > > > > ? ? ? ? for
> >> > > > > ? ? ? ? ? ? ? ? ? ?example, from Chicken, "?galGal2_dna
> >> > > > > ? ? ? ? range=chr13:13120186-13124117
> >> > > > > ? ? ? ? ? ? ? ? ? ?5'pad=0 3'pad=0 revComp=FALSE strand=?
> >> > > > > repeatMasking=False",
> >> > > > > ? ? does
> >> > > > > ? ? ? ? ? ? ? ? ? ?galGal2 means for Chicken?
> >> > > > > ? ? ? ? ? ? ? ? ? ?in mouse, "?mm4_dna
> >> range=chr6:122959016-122974672
> >> > > > > 5'pad=0
> >> > > > > ? ? ? ? 3'pad=0
> >> > > > > ? ? ? ? ? ? ? ? ? ?revComp=FALSE strand", does mm4 means mouse? in
> >> > > human,
> >> > > > > ? ? "?hg16_dna
> >> > > > > ? ? ? ? ? ? ? ? ? ?range=chr4:56214201-56291736 5'pad=0 3'pad=0
> >> > > > > revComp=FALSE ",
> >> > > > > ? ? hg
> >> > > > > ? ? ? ? ? ? means
> >> > > > > ? ? ? ? ? ? ? ? ? ?for Human? etc..
> >> > > > > ? ? ? ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? ? ? ?I mean do you have some unique character in
> >> sequences
> >> > > to
> >> > > > > ? ? ? ? respresent
> >> > > > > ? ? ? ? ? ? each
> >> > > > > ? ? ? ? ? ? ? ? ? ?unique organism? if you have, could you provide
> >> me
> >> > > the
> >> > > > > list
> >> > > > > ? ? for
> >> > > > > ? ? ? ? that?
> >> > > > > ? ? ? ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? ? ? ?thanks
> >> > > > > ? ? ? ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? ? ? ?zhaodong
> >> > > > > ? ? ? ? ? ? ? ? ? ?_______________________________________________
> >> > > > > ? ? ? ? ? ? ? ? ? ?Genome maillist  -  Genome at soe.ucsc.edu
> >> > > > > ? ? ? ? ? ? ? ? ? ?http://www.soe.ucsc.edu/mailman/listinfo/genome
> >> > > > > ? ? ? ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? ? ? --
> >> > > > > ? ? ? ? ? ? ? ? ? Vincenzo Forgetta
> >> > > > > ? ? ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? ? ?  Computational Biology
> >> > > > > ? ? ? ? ? ? ? ? ?   McGill University and Genome Quebec Innovation
> >> > > Centre
> >> > > > > ? ? ? ? ? ? ? ? ?   740 Dr. Penfield Avenue Room 7211
> >> > > > > ? ? ? ? ? ? ? ? ?   Montreal, Quebec Canada, H3A 1A4
> >> > > > > ? ? ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? ? ?   Tel: 514-398-3311 00476
> >> > > > > ? ? ? ? ? ? ? ? ?   Email: vince.forgetta at staff.mcgill.ca
> >> > > > > ? ? ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ? ? ? _______________________________________________
> >> > > > > ? ? ? ? ? ? ? ? ? Genome maillist  -  Genome at soe.ucsc.edu
> >> > > > > ? ? ? ? ? ? ? ? ? http://www.soe.ucsc.edu/mailman/listinfo/genome
> >> > > > > ? ? ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ? ? ?
> >> > > > > ? ? ? ? ?
> >> > > > > ? ?
> >> > > > > ?
> >> > > > >
> >> > >
> >> ? --------------------------------------------------------------------------
> >> > > > > --
> >> > > > > ? ? ----
> >> > > > > ? ?
> >> > > >
> >> >
> >
>

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