[Bioperl-l] parser for GeneSeqer
cjfields at uiuc.edu
Fri Jun 30 13:54:23 EDT 2006
If you plan on generating seqfeatures from this output you could
check out the Bio::Tools core modules for examples. There are a few
there that take program output and convert them to
Bio::SeqFeature::Generic objects, including Bio::Tools:RNAMotif and
Bio::Tools::tRNAscanSE. If alignments are involved you might want
something like Bio::SeqFeature::FeaturePair. Not sure about using
the SeqFeature::Annotation or others; I thought that the some of the
Annotation/Annotatable stuff might be changing soon but I may be wrong.
On Jun 30, 2006, at 12:01 PM, Robert Buels wrote:
> Hi all,
> I find myself needing a parser for GeneSeqer output, so I'm writing
> (which I will submit for your consideration when it's working). In a
> nutshell, GeneSeqer is a (kind of old) program for aligning a bunch of
> ESTs to genomic sequence, then using those alignments to predict where
> in the genomic sequence the genes are. So really what you get from
> is a bunch of hierarchical features.
> I don't really know where I should put it in the bioperl hierarchy
> though. Probably FeatureIO?
> And what's the current fashion for objects it should emit?
> Bio::SeqFeature::Generic? Bio::SeqFeature::Annotated?
> Robert Buels
> SGN Bioinformatics Analyst
> 252A Emerson Hall, Cornell University
> Ithaca, NY 14853
> Tel: 503-889-8539
> rmb32 at cornell.edu
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> Bioperl-l at lists.open-bio.org
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign
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