[Bioperl-l] parser for GeneSeqer

Chris Fields 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.

Chris

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  
> 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
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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