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.