[Genome] novel polymorphisms (fwd)

[Galt Barber]

Thanks, Daryl, for the suggestion.
That would be the track "SNPs (126)"
in the same track group where Hapmap track is found.

-Galt


---------- Forwarded message ----------
Date: Wed, 30 Jan 2008 19:56:51 -0800
From: Daryl Thomas <daryl at soe.ucsc.edu>
To: Galt Barber <galt at soe.ucsc.edu>
Subject: Re: [Genome] novel polymorphisms

The HapMap SNPs track is a subset of the dbSnp-based tracks (snp126, snp127,
snp128, ...), so the user may have better luck with one of those.


On 1/30/08 4:46 PM, "Galt Barber" <galt at soe.ucsc.edu> wrote:

>
> Start the UCSC genome browser,
> choose your lastest human assembly.
> Enter COL5A3 into the "search/position" text box
> and click the button.
>
> Now turn on the track "HapMap SNPs" which is in the
> "Variation and Repeats" group of tracks for SNP information.
> This track control is a ways down the page.
> Once you have your track turned on,
> you can click on each element.  The graphic picture
> of the chromosome is active.  Clicking on a snp will take
> you to a page with detailed info on that snp.
>
> You can turn on the "Restr Enzymes" track in the
> group "Mapping and Sequencing Tracks" which is near the top.
> This shows common restriction enzymes recognition sites.
>
> Each track can be shown in multiple levels of detail,
> i.e. hide, dense, squish, pack, full.
>
> When zooming in to the detailed base level and with
> the base position turned to full, you can see the
> individual amino acids and dna bases.
>
> You can also use the HapMap SNP track
> to show which SNPs are synonymous, non-synonymous,
> and other information about the SNP.
>
> Click on the grey "help" button to the left of the track
> to see a detailed page with configuration controls for
> many options and other detailed information about the track.
>
> -Galt
>
>
> On Wed, 30 Jan 2008, Dan Greenspan wrote:
>
>> I recently submitted a paper which included a table with 23 single
>> nucleotide polymorphisms that we had found by sequencing the coding
>> sequences and splice junctions of the COL5A3 gene in 13 patients with
>> hypermobility Ehlers-Danlos syndrome. We gave the base pair changes,
>> patient allele frequencies and patient genotype frequencies
>> (individuals homozygous for either allele or heterozygous), and
>> showed where amino acid changes and restriction site polymorphisms
>> took place. The editor suggested that none of this should be included
>> in the paper, as much if not all of these data should be readily
>> ascertainable via the UCSC genome browser. I have tried determining
>> which of these polymorphisms are ascertainable via your site, and
>> whether any might be novel - or whether any of the data we might
>> present on these polymorphisms might be useful to readers beyond what
>> they can readily get from the data bases. I have not been able to
>> figure out how to use your browser to find polymorphisms in the
>> coding sequences and splice junctions of this gene. Can someone there
>> help? I would hate to take anything out of the paper that might be
>> useful to workers in the field.
>> Thank you,
>> dan greenspan
>>
>>
>> Daniel S. Greenspan, Ph.D.
>> Professor
>> Department of Pathology and Laboratory Medicine
>> Department of Pharmacology
>> University of Wisconsin
>> 5675 MSC
>> 1300 University Avenue
>> Madison, WI  53706
>> Tel 608 262-4676
>> Fax 608 262-6691
>> dsgreens at wisc.edu
>>
>>
>>
>> _______________________________________________
>> Genome maillist  -  Genome at soe.ucsc.edu
>> http://www.soe.ucsc.edu/mailman/listinfo/genome
>>
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