[Bioperl-l] parser for GeneSeqer

[Hilmar Lapp]

No scoop b/c no time. I am busy w/ a grant and Lincoln had to leave  
early as well on Friday. Sorry.

On Jul 6, 2006, at 7:11 PM, Robert Buels wrote:

> The Annotation/Annotatable stuff was going to be talked about at the
> GMOD meeting that just happened, wasn't it?  What's the scoop on that?
>
> Rob
>
>
> Chris Fields wrote:
>> 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
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>
> -- 
> 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
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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