[Bioperl-l] program that search databais
Peter J Ulintz
pulintz@umich.edu
Tue, 3 Oct 2000 12:15:10 -0400 (EDT)
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Thanks Aaron for the C routine. I've attached a Perl version of a
subroutine to calculate pI that sounds similar to what you described.
The routine takes a string representing an AA sequence. If anyone is
interested in a python version, let me know.
--Pete
On Tue, 3 Oct 2000, Aaron J Mackey wrote:
>
> A few people have asked for this info, so I'm copying the list. Excuse
> the slightly offtopic conversation.
>
>
> On Mon, 2 Oct 2000, Aaron J Mackey wrote:
>
> >
> > 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
> > like).
> >
> > I'll send you the references and my code, if you're interested.
> >
> > -Aaron
> >
> > 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.
> > >
> >
> >
>
> --
> o ~ ~ ~ ~ ~ ~ o
> / Aaron J Mackey \
> \ Dr. Pearson Laboratory /
> \ University of Virginia \
> / (804) 924-2821 \
> \ amackey@virginia.edu /
> o ~ ~ ~ ~ ~ ~ o
>
>
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