[Bioperl-l] program that search databais

Aaron J Mackey ajm6q@virginia.edu
Mon, 2 Oct 2000 20:21:44 -0400 (EDT)

I once wrote a pI solver in Perl using a method to explicitly solve for
pI.  But it turns out it's much better to simply 'slide' from pH 0 to pH
14 and see where the electric charge function goes from negative to
positive.  While less elegant, it's much faster (and you can play tricks
with numerical derivatives near zero to get an accurate value, if you'd

I'll send you the references and my code, if you're interested.


On Mon, 2 Oct 2000, Tsvika wrote:

> 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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