[Genome] FISH probes from BAC clones
BIJU JOSEPH
bjoseph5 at jhmi.edu
Mon Feb 19 15:03:23 PST 2007
If a FISH probe has been derived from a BAC clone, how could I use the iformation to find out any related smaller size FISH probes are available commercially?
Biju Joseph
Division of Endocrinology and Metabolism
Johns Hopkins School of Medicine
Suite 813, Hunterian building
1915, East Madison st.
Baltimore, MD 21287
Phone: 410-502-3046
----- Original Message -----
From: genome-request at soe.ucsc.edu
Date: Monday, February 19, 2007 3:09 pm
Subject: Genome Digest, Vol 49, Issue 26
To: genome at soe.ucsc.edu
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> Today's Topics:
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> 1. Re: looking for human insulin gene (Archana Thakkapallayil)
> 2. Recombination rate and exon conservation (Isabelle Dupanloup)
> 3. local tool to extract region from wiggle format (Stein Aerts)
> 4. Blat on Configure screen (Michel Weber)
> 5. Re: local tool to extract region from wiggle format
> (Hiram Clawson)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 18 Feb 2007 22:24:53 -0800
> From: Archana Thakkapallayil <archanat at soe.ucsc.edu>
> Subject: Re: [Genome] looking for human insulin gene
> To: "Bhattacharyya, Nisan (NIH/NIDDK) [E]"
> <NisanB at intra.niddk.nih.gov>
> Cc: genome at soe.ucsc.edu
> Message-ID: <45D942B5.4090600 at soe.ucsc.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hello Nisan,
>
> To get this information, open the genome browser to the most recent
> human assembly (hg18) and then enter the name of the insulin
> producing
> gene, "INS" into the position/search box. This opens a page with list
> of
> Known Genes with hyperlink to the Known Genes track in the browser.
> From
> this page, click on the first link, "INS (NM_000207) at
> chr11:2137585-2139000 - proinsulin precursor". Then turn on the BAC
> End
> Pairs track in the browser. You should see several BACs near your
> gene
> of interest. Choose the one(s) that work best for you and click
> directly on the picture of the BAC End Pair.This will take you to a
> page
> on the UCSC site that contains details about that particular BAC End
>
> Pair. The clone name at the top of this page is a link to the NCBI
> Clone Registry for that BAC. The following NCBI page will have a link
> to
> the Distributor Information, if any.
>
> Hope this is helpful to you. Please let us know if you have further
> questions.
>
> Regards,
>
> Archana
> UCSC Genome Bioinformatics Group
>
>
> Bhattacharyya, Nisan (NIH/NIDDK) [E] wrote:
> > Hi:
> >
> >
> >
> > My name is Nisan and I am looking for human insulin gene in chromosome
> > 11 (11p15.5 may be).
> >
> > I want to find a BAC clone for this region and I wonder whether you
> can
> > help me on this matter.
> >
> > I wonder whether you can write me back or call me at 301-496-6911.
> >
> > Nisan
> >
> > _______________________________________________
> > Genome maillist - Genome at soe.ucsc.edu
> >
> >
>
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 19 Feb 2007 09:03:13 +0100
> From: "Isabelle Dupanloup" <isabelle.dupanloup at zoo.unibe.ch>
> Subject: [Genome] Recombination rate and exon conservation
> To: <genome at soe.ucsc.edu>
> Message-ID: <001c01c753fc$67ac7d50$8f8a5c82 at cmpg.unibe.ch>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi there,
>
> I have 2 questions regarding the use of data made available by the UCSC
> Genome Bioinformatics group.
>
> 1) I'm interested in getting recombination rates, for the human genome,
> along the different chromosomes. I saw that you made available different
> tables in the Download section of the UCSC genome website. And here is
> my question. What are the differences between these tables:
> - hapmapRecombRate.txt.gz
> - snpRecombRateHapmap.txt.gz ?
> These 2 tables contain essentially the same info but the coordinates
> of
> the genomic segments are slightly different, as well as the line
> numbers. Do you have an explanation for that ?
>
> 2) I would like to know something about exons conservation in vertebrate
> species. What I need to do is to check if an exon of a gene in the human
> genome is present also in the genome of chimp, macaque, mouse, rat,
> chicken etc. (and do that for a lot of human exons). I know that you
> make available different kind of genomic alignments for different sets
> of species. But do you make available somewhere a table listing the
> presence of human exons in different vertebrate species' genome ? If
> it
> is not the case, do you have an advice for the best table I need to
> download to get what I need ?
>
> Thank you very much for your help.
>
> Isabelle
>
> -------------------
> Isabelle Dupanloup PhD
> Computational and Molecular Population Genetics Group Baltzerstrasse
> 6
> 3012 Bern Switzerland
> Tel: +41 31 631 45 49
> Fax: +41 31 631 48 88
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 19 Feb 2007 14:41:13 +0100
> From: Stein Aerts <stein.aerts at med.kuleuven.be>
> Subject: [Genome] local tool to extract region from wiggle format
> To: genome at soe.ucsc.edu
> Message-ID: <45D9A8F9.4060006 at med.kuleuven.be>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi,
> Is there perhaps a Kent utility to extract all scores within a
> chromosomal range from a WIG formatted file?
>
> Many thanks and best regards,
> Stein
>
> --
> Stein Aerts, PhD
> Laboratory of Neurogenetics
> Department of Molecular and Developmental Genetics
> VIB - University of Leuven
> Herestraat 49, bus 602
> 3000 Leuven, Belgium
> Tel. +32(16)330132
> Fax. +32(16)347190
>
>
>
> Disclaimer:
>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 19 Feb 2007 16:01:06 +0100
> From: Michel Weber <Michel.Weber at ibcg.biotoul.fr>
> Subject: [Genome] Blat on Configure screen
> To: genome at soe.ucsc.edu
> Message-ID: <5.0.2.1.2.20070219155441.019f17f0 at pop.biotoul.fr>
> Content-Type: text/plain; charset="iso-8859-1"; format=flowed
>
> On the Configure screen of the human browser, I don?t see ?Blat
> sequence?
> among the ?Mapping and Sequencing tracks?. Is it possible to add this?
>
> Thanks in advance
>
> Michel
>
>
> Michel WEBER
> Laboratoire de Biologie Mol?culaire Eucaryote
> Toulouse France
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 19 Feb 2007 09:35:42 -0800
> From: Hiram Clawson <hiram at soe.ucsc.edu>
> Subject: Re: [Genome] local tool to extract region from wiggle format
> To: Stein Aerts <stein.aerts at med.kuleuven.be>
> Cc: genome at soe.ucsc.edu
> Message-ID: <4971ad10ffcdcec0eb1142260b69dd0b at soe.ucsc.edu>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
> Good Morning Stein:
>
> Please refer to the program: hgWiggle
> You can build this in the source tree directory:
> src/hg/makeDb/hgLoadWiggle/
>
> --Hiram
>
> On 2007 Feb 19, , at 5:41 AM, Stein Aerts wrote:
>
> > Hi,
> > Is there perhaps a Kent utility to extract all scores within a
> > chromosomal range from a WIG formatted file?
> >
> > Many thanks and best regards,
> > Stein
> >
> > --
> > Stein Aerts, PhD
> > Laboratory of Neurogenetics
> > Department of Molecular and Developmental Genetics
> > VIB - University of Leuven
> > Herestraat 49, bus 602
> > 3000 Leuven, Belgium
> > Tel. +32(16)330132
> > Fax. +32(16)347190
> >
> >
> >
> > Disclaimer:
> >
> > _______________________________________________
> > Genome maillist - Genome at soe.ucsc.edu
> >
> >
>
>
>
> ------------------------------
>
> _______________________________________________
> Genome maillist - Genome at soe.ucsc.edu
>
>
>
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