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From: webb@bx.psu.edu Date: March 5, 2010 1:44:01 PM EST To: Tjaart de Beer <tdebeer@gmail.com> Cc: Anton Nekrutenko <anton@bx.psu.edu>, Webb Miller <webb@bx.psu.edu>, Aakrosh Ratan <ratan@cse.psu.edu> Subject: Re: Fwd: [galaxy-user] Protein names

Hi,

The gene annotations are from RefSeq. As we processed the SNPs with tools such as PolyPhen and Sift, we sometimes had to use other names. My assumption was that people would load their favorite gene annotations into Galaxy and use an "interval" join to attach the desired names. Can you do something like that? Or is the problem that you need to deal with alternate splice forms?

Please keep asking until you have everything working. If necessary, I can regenerate the file with other protein names. Thanks for your patience.

--Webb

Quoting Anton Nekrutenko <anton@bx.psu.edu>:

...

Webb:

The question here is on where the protein names come from. Can you elaborate, so I send him a reply.

Thanks,

anton

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From: Tjaart de Beer <tdebeer@gmail.com> Date: March 5, 2010 7:34:13 AM EST To: galaxy-user@bx.psu.edu Subject: [galaxy-user] Protein names

Hi

I am trying to parse some data from the Bushmen dataset and have a question.

Where do you get the protein names from? It does not correspond 100% to the UniProt ID field in Uniprot entries nor is it Uniprot AC numbers. Is there some kind of mapping I can use to get the appropriate names or Uniprot entries? Would you be able to provide with this mapping? I have been going through the Uniprot website rather extensively and have failed to find any such downloadable mapping. Hope you can help!

Thanks!

Dr. Tjaart de Beer Thornton group EMBL-EBI Cambridge _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user

Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org