[BiO BB] RefSeq ids to gene names
marchywka at hotmail.com
Mon Nov 24 18:14:46 EST 2008
Generally for things like this, it can be easier to download a flat text file of the db contents and use grep to get what you want. I used to do this with eutilz results and now use for other db sources.
Does the source file exist as a zip on their ftp site? Just download that and use Cygwin grep and sed.
From: Charles Danko
To: bbb at bioinformatics.org
Sent: Nov 24, 2008 5:18 PM
Subject: Re: [BiO BB] RefSeq ids to gene names
I don't think that those are RefSeq IDs.
In general, the easiest way to do something like this is using
biomart: http://www.biomart.org/ <http://www.biomart.org/> .
1. Go to martview.
2. Select the database and species.
3. Do NOT change the selection under filters.
5. Under attributes, select any ID type that you want.
The result will be a table of ID associations that you can export in
the format of your choice...
On Mon, Nov 24, 2008 at 1:31 PM, Gaurav Pandey <pandey.gaurav at gmail.com> wrote:
> Where can I get a text/excel file with a mapping of RefSeq id's to their
> common gene names (such as SYN2, SERPINA3 etc), particularly for homo
> sapiens? The NCBI ftp site was not extremely useful.
> Also, some of the RefSeq IDs I have are of the form 'Contig30743_RC'. Are
> these also RefSeq IDs?
> Any help will be deeply appreciated. Thanks!
> Gaurav Pandey Email: gaurav at cs.umn.edu
> Computer Science Department Webpage: www.cs.umn.edu/~gaurav <http://www.cs.umn.edu/~gaurav>
> University of Minnesota Tel: 612-701-2494
> BBB mailing list
> BBB at bioinformatics.org
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