[Bioperl-l] program that search databais

Mon, 02 Oct 2000 16:06:22 -0400

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Hi all,

I am writing a Perl program that search proteins  database, and
find matches according predicted Molecular Wight (MW) versus MW
from results of Mass spectrometry. Also, the program takes short
amino acid sequence (tag) and looks at the N-term or C-term as
you like. The program has MW tolerance (+/-X%), and uses regexp
for the tag input. The program is fully functional, and I used it
on C.elegans wormpep25 successfully.
Now I want to add the P.I., isoelectric point, option. So, like
MW, one can try to find matches according to the P.I. results of
first dimension of 2D gel versus the predicted P.I.
I would appreciate if you could help me with P.I. calculations,
and algorithms. Also, I would like to hear if you think it is a
start for Proteomics applications in bioperl?

Tsvika.

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<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
<html>
<tt>Hi all,</tt><tt></tt>
<tt>I am writing a Perl program that search proteins&nbsp; database,
and</tt>
 <tt>find matches according predicted Molecular Wight (MW) versus MW</tt>
 <tt>from results of Mass spectrometry. Also, the program takes short</tt>
 <tt>amino acid sequence (tag) and looks at the N-term or C-term as</tt>
 <tt>you like. The program has MW tolerance (+/-X%), and uses regexp</tt>
 <tt>for the tag input. The program is fully functional, and I used
it</tt>
 <tt>on C.elegans wormpep25 successfully.</tt>
 <tt>Now I want to add the P.I., isoelectric point, option. So, like</tt>
 <tt>MW, one can try to find matches according to the P.I. results of</tt>
 <tt>first dimension of 2D gel versus the predicted P.I.</tt>
 <tt>I would appreciate if you could help me with P.I. calculations,</tt>
 <tt>and algorithms. Also, I would like to hear if you think it is a</tt>
 <tt>start for Proteomics applications in bioperl?</tt><tt></tt>
<tt>Tsvika.</tt></html>

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n:Greener;Dr. Tsvika
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