Fwd: [galaxy-dev] Fwd: Protein names
Begin forwarded message:
From: Yu Lin <linikujp@gmail.com> Date: March 5, 2010 7:21:09 PM EST To: Anton Nekrutenko <anton@bx.psu.edu> Subject: Re: [galaxy-dev] Fwd: [galaxy-user] Protein names
Hi,
"My assumption was that people would load their favorite gene annotations " from the ontology's point of view: "favorite gene annotations" will be dangerous. "use an "interval" join to attach the desired names".... what dose it mean?
Dangerous means that later there will be a lot misunderstandings, which is not convenient for biologist. I think it's better to use a standard. OR favorite gene annotations always bound to a standard gene annotations.
Thanks, Lin.
************************************************* Yu Lin Ph.D.,M.D.
Genome Resource and Analysis Unit, Genomics Laboratory, Center for Developmental Biology, RIKEN
TEL&FAX 0081-78-3063048 Extension:4232 Email: linyu@cdb.riken.jp *************************************************
2010/3/6 Anton Nekrutenko <anton@bx.psu.edu>:
Begin forwarded message:
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
Begin forwarded message:
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
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Anton Nekrutenko
Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org
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