[Bioperl-l] est2genome and bioperl

[Jason Stajich]

Not yet - there is one in Ensembl we could probably lift - either way
AFAIK this is a very trivial format to parse so would be very simple to
write one.  Not sure how to handle multiple good hits in a segment in
terms of stitching them into a gene - but again ensembl has probably deal
with this.

We've not really fleshed out the Bio::SeqFeature::Exon,
Bio::SeqFeature::Gene objects (Hilmar should these perhaps feed better
with the Bio::Tools::Prediction::Exon objects or be combined?).


while( <DATA> ) {
 next if( /^\s+/);
 my ($feattype,$len,$score,$hs,$he,$hit,$qs,$qe,$query) = split;

 # Build Bio::SeqFeature::Generic or perhaps Bio::SeqFeature::Exon objects
}

__DATA__
Exon       652 100.0     5   656 AF243532.1    1004  1655 Contig4614
Span       652 100.0     5   656 AF243532.1    1004  1655 Contig4614
Segment    652 100.0     5   656 AF243532.1    1004  1655 Contig4614

-jason


On Tue, 1 Oct 2002, Charles Plessy wrote:

> Hello,
>
> I'd like to compare the results of est2genome on two sets of sequences
> (ests, and clusters), in order to identify sequences that are
> really likely to be part of the same gene.
>
> (I'm working with zebrafish, and since the genome is partially
> duplicated, it's hard to tell if we deal with geneX.1 or geneX.2 when
> it's homologous to a mamalian geneX. In addition, I don't have any
> idea of the reliability of automatic clusterings in zebrafish for this
> same reason.)
>
> My question is : is there a parser of est2genome output implemented in
> bioperl? From a google search, I would say no, but...
>
> Thanks,
>
> Charles
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>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu