[Bioperl-l] simplealign, prediction parsers

[Richard Adams]

Heikki,
I'll tidy up the Simple::Align->purge code and send it to you asap.
Re parsers for netphos, psort etc. Basically  I'm working with about 30-40
genes on chromosome 4
in a region associated with bipolar disorder. I'm trying to build up a
database of possibly important
functional residues/regions of the proteins for prioritising the
experimental analysis of SNPs within
the coding region of the genes. Also I'm hoping to bolster the prediction
accuracy of these
programs by looking for conservation of prediction between sequence
homologues in a Clustal alignment.

So that's why I'm developing the parsers. At present they are not in the
BioPerl 'format' at all and are standalone
modules/subroutines. I've not contributed to BioPerl before - is there a
standard way that you want code contributed in
or is some assistance likely to be available from someone more experienced
with BioPerl guts than myself?

Richard

Heikki Lehvaslaiho wrote:

> Richard,
>
> Bio::SimpleAlign::purge() has not been functional as far as I know. We
> do not even have tests for it. Please send me your fixes and add them in
> and add you as an contributor to the module.
> It would be even better of you have written tests into t/SimpleAlign.t,
> too!
>
> It has been a while since you posted your message and there has been no
> answers to it. I think it can be safely said that no one else is working
> on Psort, TargetP or netphos parsers. It would be great to have them.
> Let us know what your plans are.
>
>         -Heikki
>
> On Tue, 2002-08-27 at 11:51, Richard Adams wrote:
> >     Hello,
> > Please ignore this if it's already been fixed but there seems to be 2
> > problems in 1.0.2
> > with Bio::SimpleAlign purge function.
> >
> > 1.  the get_nse call produces the error
> >     Use of uninitialized value in numeric eq (==) at
> > /packages/perl/lib/site_perl/5.6.0/Bio/SimpleAlign.pm line 373, <GEN0>
> > line 242.
> > 2.
> >     the lines
> > @one = $seq->seq();
> >    @two = $seq2->seq();
> >     I guess are supposed to be split so that each element is an amino
> > acid or - or .
> >     But the way the code works there will only be one element - the
> > whole sequence string.
> >
> > I've fixed these problems for my own use so if my code would be any use
> > I'd gladly submit it.
> >
> >
> >
> > I'm writing some parsers for various prediction servers, such as
> > Expasy's Psort, TargetP, netphos and ultimately plan to develop parsers
> > for some secondary
> > structure prediction servers.  Are people already working on this sort
> > of thing or would these be useful additions?
> >
> > Richard
> >
> > Dr Richard Adams
> > Molecular Medicine Centre
> > University of Edinburgh UK
> >
> >
> > _______________________________________________
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> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> --
> ______ _/      _/_____________________________________________________
>       _/      _/                      http://www.ebi.ac.uk/mutations/
>      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
>     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
>    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
>   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
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