[Bioperl-l] SeqFeature::Similarity

Hilmar Lapp hlapp@gmx.net
Tue, 01 Aug 2000 02:56:57 +0200

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.

Hilmar Lapp                                      email: hlapp@gmx.net
NFI Vienna, IFD/Bioinformatics                   phone: +43 1 86634 631
A-1235 Vienna                                      fax: +43 1 86634 727