I'm trying to collect all protein coding sequences from various species.
I start here: http://www.biomart.org/biomart/martview/
My selections are as follows:
Database: Ensembl Genes 66 (Sanger UK)
Dataset: Homo sapiens genes (GRCh37.p6)
Filters: Gene Type: protein coding
Attributes: Sequences/Coding Sequences
Header: Associated Gene Name, Description, Ensembl Gene ID
When I click on "Count" I get 21405/56478, which I interpret as 21405
coding sequences that I should be recovering out of a total of 56478
entries.
I click "Results", "Unique Results Only", "Export" to "Compressed Web file
(notify by email), I enter my email address, then "Go".
The resulting file I download is 111,827 Kb in size and it contains 98,024
entries, many more than the 21,405 I expected. (I determined this by
doing a "seach and replace" for ">"). The first entry is gene name
"CYP26B1", and I find a total of five separate entries with this name and
with identical gene descriptions and Ensemble Gene IDs. The five
sequences, however, are different, although three of them are identical
through the first few lines.
So what am I doing wrong? When I went through the same steps for E. coli
K12 I recovered a file with 4258 sequences, the number I expected based
on the output of "Count".
Thanks,
George Gutman
Cheers,
George Gutman
*************************************************************************
* George A. Gutman, Professor Emeritus *
* Department of Microbiology and Molecular Genetics *
* University of California, Irvine *
* Office: (949)824-6593 B250, Med Sci *
* (714)552-1242 (cell) e-mail: [email protected] *
* http://www.ucihs.uci.edu/microbio/facultyResearch/faculty/gutman.html *
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On Thu, 3 May 2012, Arek Kasprzyk wrote:
> Date: Thu, 3 May 2012 12:55:22 -0400
> From: Arek Kasprzyk <[email protected]>
> To: George Gutman <[email protected]>
> Cc: [email protected]
> Subject: Re: [BioMart Users] Where to address questions
>
> Dear George,
> please feel free to post here and we'll try to help you. Please give us
> more details on your problem, the portal that you are using etc
>
>
> a
>
> On Wed, May 2, 2012 at 2:30 AM, George Gutman <[email protected]> wrote:
>
> > I'm trying to download collections of protein coding regions from various
> > genomes and am having trouble. Where can I address my questions? Do I
> > need to be a member of this list to post here?
> >
> > George Gutman
> > _______________________________________________
> > Users mailing list
> > [email protected]
> > https://lists.biomart.org/mailman/listinfo/users
> >
>
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