[Bioperl-l] program that search databais
Aaron J Mackey
ajm6q@virginia.edu
Tue, 3 Oct 2000 22:28:05 -0400 (EDT)
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Just to be explictly clear to the onlookers - Peter's code uses the second
approach I mentioned - iteratively "searching" for the pH where the net
charge equals 0. The c code I sent along solves for pI explictly via the
Sillero algorithm. Your mileage may vary.
-Aaron
On Tue, 3 Oct 2000, Peter J Ulintz wrote:
>
> 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
> >
> >
>
--
o ~ ~ ~ ~ ~ ~ o
/ Aaron J Mackey \
\ Dr. Pearson Laboratory /
\ University of Virginia \
/ (804) 924-2821 \
\ amackey@virginia.edu /
o ~ ~ ~ ~ ~ ~ o
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