Friday, August 6, 2010

structure for packages retrieving online alignment sequences

The aim of this package is to provide convenient methods to retrieving online alignment sequences for the BioPerl users. The alignment sequences are converted into Bio::SimpleAlign object after the retrieval, which will be easy to manipulate and write to local disk.

Here is the structure of the packages:
Bio::DB::Align (interface, and calling other packages)
Bio::DB::Align::Pfam (retrieving alignment from Pfam)
Bio::DB::Align::Rfam (retrieving alignment from Rfam)
Bio::DB::Align:Prosite (retrieving alignment from Prosite)
Bio::DB::Align:ProtClustDB (retrieving alignment from Entrez Protein Clusters Database)

Usually four methods are provided for each package:
get_Aln_by_id (retrieving alignment by id and returns Bio::SimpleAlign object)
get_Aln_by_acc (retrieving alignment by acession and returns Bio::SimpleAlign object) (Rfam and Prosite only supports this method)
id2acc (id to accession conversion)
acc2id (accession to id conversion)

These packages are built dependent on LWP::UserAgent, HTTP::Request and Bio::DB::GenericWebAgent. Bio::DB::Align::ProtClustDB is dependent on Bio::DB::EUtilities.

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