[Bioperl-l] Bio::SeqFeature::GeneStructure and Prediction

[James Gilbert]

Hilmar,

I'd like to see the Ensembl Gene structure in
BioPerl, because I think it is more or less
correct.  In Ensembl a Gene has one or many
Transcripts, each of which can have a Translation,
and each Transcript has one or many Exons.  
Transcripts share exons, and so you can get a
non-redundant list of exons from a gene.  So I'd
like to see a Transcript layer in there somewhere.

	James

On Wed, 2 Aug 2000, Hilmar Lapp wrote:

> Following up the discussion from yesterday, I've added a
> Bio::SeqFeature::GeneStructure module, offering specific support for
> representing the structure or structural elements of a gene. I tried to keep
> it rather generic, so there aren't really that fancy things. Most of the
> methods deal with managing data elements in a convenient way. There are some
> basic 'computations' though, like a introns() method returning the regions
> intervening the exons as features, and a cds() method concatenating the
> respective sequences of exons.
> 
> Note that this module doesn't know about prediction, and doesn't care about
> the actual type of the exon objects or other structural elements being added,
> as long as they implement Bio::SeqFeatureI.
> 
> Bio::SeqFeature::GeneStructure is-a Bio::SeqFeature::Generic.
> 
> Regarding prediction (my present goal is representing gene structure
> prediction results), I opened a directory Bio/Tools/Prediction (make sure you
> say 'cvs update -d'), meant to hold any modules specific to prediction
> methods. There I've created two modules Bio::Tools::Prediction::Gene and
> Bio::Tools::Prediction::Exon.
> 
> Bio::Tools::Prediction::Gene is-a Bio::SeqFeature::GeneStructure with support
> for being a predicted gene structure: there are methods to store a predicted
> CDS and a predicted peptide sequence. It is not required to but will usually
> have objects of Bio::Tools::Prediction::Exon added as exons.
> 
> Bio::Tools::Prediction::Exon is-a Bio::SeqFeature::Generic with support for a
> predicted exon. That is, there are several methods for various scores
> (start-of-exon score, which may be an acceptor splice site score, end-of-exon
> score which may be a donor splice site score, etc).
> 
> A Bio::Tools::Genscan will follow utilizing the above modules. Similarly, an
> MZEF parser. ESTScan in principle predicts gene structural elements, too,
> namely coding and uncoding regions, and predicts peptide sequences, so I hope
> I can use this model for that, too.
> 
> Have a look if you're interested, and I'd appreciate feedback.
> 
> 	Hilmar
> -- 
> -----------------------------------------------------------------------
> Hilmar Lapp                                      email: hlapp@gmx.net
> NFI Vienna, IFD/Bioinformatics                   phone: +43 1 86634 631
> A-1235 Vienna                                      fax: +43 1 86634 727
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James G.R. Gilbert
The Sanger Centre
Wellcome Trust Genome Campus
Hinxton
Cambridge                        Tel: 01223 494906
CB10 1SA                         Fax: 01223 494919