[Bioperl-l] 0.9.0 released
Fri, 10 Aug 2001 14:41:18 -0400 (EDT)
I have put bioperl developer release 0.9.0 in
This release has new modules Bio::Tools::Run::RemoteBlast, Bio::DB::EMBL,
and the beginnings of interfaces for running external programs in a
uniform manner. Will will be working attaching to Martin Senger's Novella
interface and with the EMBOSS suite of applications first and branch out
to other applications where possible. There is also a standalone GFF DB
in Bio::DB::GFF by Lincoln Stein suitable for a DAS backend.
The API for a developer release is less stable than the traditional
bioperl releases. The next stable release will be bioperl 1.0 coming out
in late 2001. Please realize the modules here may have bugs and may add
or lose functionality between 0.9.x releases. The developer releases are
an easy way to get a snapshot of the current bioperl development cycle and
know that at least all tests pass. This release should not be used in a
Jason Stajich on behalf of the bioperl developers.
Here are the notes from the Changelog.
0.9.0 Developer's release
o perl version at least 5.005 is now required instead of perl 5.004
o Bio::Tools::Run::RemoteBlast is available for running remote
blast jobs at NCBI.
o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
Also added are related modules UTR3, UTR5, Exon, Intron,
Promotor, PolyA and Transcript.
o Speedup of translate method in PrimarySeq
o Bio::SimpleAlign has new methods: location_from_column(), slice(),
select(), dot(), get_seq_by_pos(), column_from_residue_number()
o Various fixes to Variation toolkit
o Bio::DB::EMBL provides database access to EMBL sequence data.
Bio::DB::Universal provides a central way to point to indexes
and dbs in a single interface.
o Bio::DB::GFF - a database suitable for running DAS servers locally.
o Bio::Factory::EMBOSS is still in design phase as is
o Dia models for bioperl design are provided in the models/ directory