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: [email protected] 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 <[EMAIL PROTECTED]> 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: [EMAIL PROTECTED] > 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 > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb > <http://www.bioinformatics.org/mailman/listinfo/bbb> > _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb <http://www.bioinformatics.org/mailman/listinfo/bbb> Sent from my Verizon Wireless BlackBerry _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
