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