[Bioperl-l] SeqFeature::Similarity

[Ewan Birney]

On Tue, 1 Aug 2000, Hilmar Lapp wrote:

> I've added two new modules Bio::SeqFeature::Similarity and
> Bio::SeqFeature::SimilarityPair which at least in the short run should help in
> bridging the gap between similarity search result objects and sequence
> features. Both classes offer more specific support for the properties of a
> similarity search result, or 'hit'. Please have a look if you're interested.
> Feedback appreciated, even though I must admit that for the time being
> documentation is sparse.
> 
> Both classes could also be used as base classes for the BPlite modules, with
> more convenient and cleaner methods for storing various common properties of
> search hits.
> 
> Bio::SeqFeature::Similarity is-a Bio::SeqFeature::Generic, and
> Bio::SeqFeature::SimilarityPair is-a Bio::SeqFeature::FeaturePair. The latter
> has two Similarity objects.
> 
> In addition, there is a method to construct SimilarityPair objects from Blast
> result objects, namely from Bio::Tools::Blast::Sbjct and
> Bio::Tools::Blast::HSP objects. This is however likely to go into a separate
> class in the Bio::SeqFeatureProducer hierarchy, as discussed with Jason.
> Anyway, it's been tested and it works so far.
> 


This sounds great. We should also move the HMMER:: objects across to using
SimilarityPair and Similarity 


We are going to need to have some careful documentation in the different
sequence feature objects to guide first time users to the right object to
use. 



> 	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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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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