[BiO BB] RefSeq ids to gene names

[Mike Marchywka]

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.
------Original Message------
From: Charles Danko
To: bbb at bioinformatics.org
Sent: Nov 24, 2008 5:18 PM
Subject: Re: [BiO BB] RefSeq ids to gene names

Hi, Gaurav,
 
 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...
 
 Good luck!
 Charles
 
 On Mon, Nov 24, 2008 at 1:31 PM, Gaurav Pandey <pandey.gaurav at gmail.com> wrote:
 > Hello,
 >
 > 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
 >
 > --
 > 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
 > http://www.bioinformatics.org/mailman/listinfo/bbb <http://www.bioinformatics.org/mailman/listinfo/bbb> 
 >
 
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