[Bioperl-l] parser for GeneSeqer

Robert Buels rmb32 at cornell.edu
Fri Jun 30 13:01:38 EDT 2006


Hi all,

I find myself needing a parser for GeneSeqer output, so I'm writing one 
(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 this 
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?

Rob

-- 
Robert Buels
SGN Bioinformatics Analyst
252A Emerson Hall, Cornell University
Ithaca, NY  14853
Tel: 503-889-8539
rmb32 at cornell.edu
http://www.sgn.cornell.edu




More information about the Bioperl-l mailing list