[Bioperl-l] Human membrane proteins?

Tsvika tsvikag@helix.nih.gov
Sat, 04 Nov 2000 15:48:33 -0500


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Hi,

I would like to search the most updated and accurate Human
protein database for membrane proteins. I did it by searching via
the title line of genpept.fasta and OWL.fasta (may 1999) using this
regex:
(human(.*)membrane)(membrane(.*)human)
However, the results contained non-relevant sequences, and
probably I missed a lot of membrane proteins because the
limitation of searching the title.

(1) I wonder if there are some special human membrane protein
databases?
(2) Is there any better way to search via the actual sequences
(easy perl algorithm) and not via the title, for putative
membrane proteins?
(3) Since the NCBI OWL is from May 1999, do you know any better?

Thanks in advance for your help,

Tsvika :)

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<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
<html>
<tt>Hi,</tt><tt></tt>
<p><tt>I would like to search the most updated and accurate Human</tt>
<br><tt>protein database for membrane proteins. I did it by searching via</tt>
<br><tt>the title line of genpept.fasta and OWL.fasta (may 1999) using
this regex:</tt>
<br><tt>(human(.*)membrane)&brvbar;(membrane(.*)human)</tt>
<br><tt>However, the results contained non-relevant sequences, and</tt>
<br><tt>probably I missed a lot of membrane proteins because the</tt>
<br><tt>limitation of searching the title.</tt><tt></tt>
<p><tt>(1) I wonder if there are some special human membrane protein</tt>
<br><tt>databases?</tt>
<br><tt>(2) Is there any better way to search via the actual sequences</tt>
<br><tt>(easy perl algorithm) and not via the title, for putative</tt>
<br><tt>membrane proteins?</tt>
<br><tt>(3) Since the NCBI OWL is from May 1999, do you know any better?</tt><tt></tt>
<p><tt>Thanks in advance for your help,</tt><tt></tt>
<p><tt>Tsvika :)</tt></html>

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