[Genome] download a small sequence from mouse build 33 (May 2004)

[Kayla Smith]

Hello Again Gerald,

I made a mistake in my reply to you this morning.   We do have a SNP 
track for the mm5 (NCBI build 33) assembly.

You can skip the liftOver instructions, and go directly to making a 
Custom Track and using the Table Browser.  Let me know if you need any 
assistance with this.

Kayla Smith
UCSC Genome Bioinformatics Group


Kayla Smith wrote:
> Hello Gerald,
> 
> Your coordinates from mouse build 33 correspond to our "mm5" mouse 
> assembly.   You'll need to lift those coordinates to our "mm8" assembly 
> first.  You can find the liftOver tool by clicking on "Utilities" on the 
> blue bar on the left hand side of the main page, or by clicking here:
> 
> http://genome.ucsc.edu/cgi-bin/hgLiftOver
> 
> The reason for this is that we do not offer a SNP track for older mouse 
> assemblies.  We do offer a SNP track for both mm8 and mm9, the two most 
> recent mouse assemblies.
> 
> Here I would save your new set of coordinates as a Custom Track. 
> Details on custom tracks are here:
> 
> http://genome.ucsc.edu/cgi-bin/hgCustom
> 
>  From here, you can use the Table Browser to access the SNP table.   The 
> Table Browser is found via the "Tables" link on the blue bar on the top 
> of the main page.   Use the following settings:
> 
> clade:  Vertebrate
> genome: Mouse
> assembly:  Feb 2006
> group:  Variation and Repeats
> track:  SNPs(126)
> table: snp126
> region: genome
> intersection:  create
>    group:  custom tracks, and select your track
> output format:  all fields from selected table (you could also select 
> "sequence" here)
> click on "get output"
> 
> I am not sure whether you have a list of RS numbers, or if you just have 
> some coordinates.  The way to retrieve data is going to be different in 
> each case.  Also, you may want flanking sequence around your snps.   The 
> answer above should get you started with our tools.   I hope this is 
> helpful to you.  If you need more help, please don't hesitate to write 
> back to us.
> 
> Kayla Smith
> UCSC Genome Bioinformatics Group
> 
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> Gerald Bothe wrote:
>> I have SNPs with base coordinates from mouse build 33, e.g. mm33-17-66541888. I know how to view the sequence in the browser, but how do I download it? The sequence on the screen seems to be in a bitmap format, not text that I could just copy and past.
>>
>> Gerald
>>
>>
>>
>>
>> Gerald W. Bothe, Ph. D. 
>> Senior Scientist, R&D 
>> Taconic Biotechnology 
>> 5 University Place 
>> Rensselaer, NY 12144 
>> (518) 257 2030 ext. 12126 
>>
>>
>>
>> _______________________________________________
>> Genome maillist  -  Genome at soe.ucsc.edu
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> 
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