[Biodevelopers] RE: Subcellular loaclization - Biodevelopers Digest, Vol 8, Issue 1

[Jennifer Gardy]

Hi Ethan et al

I work on bacterial subcellular localization prediction, and at the
PSORT.org site that our group maintains (http://www.psort.org), you'll find
an extensive list of links to predictive tools for both prokaryotes and
eukaryotes.

There are multiple tools available for eukaryotic protein prediction, and of
the many choices I recommend Proteome Analyst
(http://www.cs.ualberta.ca/%7Ebioinfo/PA/Sub/index.html). It uses an
annotation keyword-based approach to prediction, wherein it finds homologs
to your query protein in SwissProt and passes keywords from the homologs'
SwissProt entries to a machine learning-based classifier. I would also
recommend trying a few other methods and collating the results to form a
consensus prediction.

You can try using signal peptide-based methods, but you have to screen your
dataset and remove any membrane proteins beforehand, so these don't get
erroneously predicted as organellar.

BLASTing your sequences against a database of proteins with annotated
localization sites also works quite well - in PSORTb we carry out an
analysis using this technique, which requires a hit at an e value less than
e-10 and for the HSP region to span at least 80% of the length of the query
and the subject (avoiding matches to a single domain of a protein).

Hope that helps, and don't hesitate to drop me a line if you need any
further advice on the subject.

Cheers
Jenn
-----------------------------
Jennifer Gardy, PhD Candidate
The Brinkman Lab
Simon Fraser University
Ph. 604 291 5414
www.sfu.ca/~jlgardy
-----------------------------


-----Original Message-----
From: biodevelopers-bounces+jlgardy=sfu.ca at bioinformatics.org
[mailto:biodevelopers-bounces+jlgardy=sfu.ca at bioinformatics.org] On Behalf
Of biodevelopers-request at bioinformatics.org
Sent: Thursday, November 24, 2005 9:00 AM
To: biodevelopers at bioinformatics.org
Subject: Biodevelopers Digest, Vol 8, Issue 1

Message: 1
Date: Wed, 23 Nov 2005 14:21:40 -0600
From: "Ethan Strauss" <ethan.strauss at promega.com>
Subject: [Biodevelopers] Subcellular localization?
To: <biodevelopers at bioinformatics.org>
Message-ID:
	<D8D8119118899D4A8EB5AD9BD24C1932011322E6 at MADMSG003.promega.com>
Content-Type: text/plain;	charset="us-ascii"

Hi, 
   I have a list of about 2500 accession numbers from Genbank Refseq.
All of them are human coding sequences and I can easily get the complete
sequence and other information from Genbank, but I can't figure out a
way to get subcellular localization information. I have pulled some data
from UniProt and from DBSubLoc
(http://www.bioinfo.tsinghua.edu.cn/dbsubloc.html) and have been able to
match about 10% of my sequences to subcellular localizations from these
databases, but that still leaves about 90% unknown. One problem is that
I can't find a way to match Genbank Accession # with the IDs in
Swiss-Prot and DBSubLoc. I have just gone on sequence identity (So far I
only call it a match when it is 100% identical). 
Do you have any ideas about how I can get subcellular localization info
for the rest of my sequences? 
Thanks for any help or suggestions!
Ethan

Ethan Strauss Ph.D.
Bioinformatics Scientist
Promega Corporation
2800 Woods Hollow Rd.
Madison, WI 53711
608-274-4330
800-356-9526
ethan.strauss at promega.com