[Bioperl-announce-l] Bioperl 1.2.2 released

Heikki Lehvaslaiho heikki at ebi.ac.uk
Tue Jul 8 16:06:30 EDT 2003

This is a bug fix release from the stable branch.

The Bioperl release 1.2.2 is available at


and is propagating around CPAN now.

Bioperl-run is a collection of modules that wrap bioinformatics
applications to allow running them from bioperl. The release cycle of
bioperl-run follows the core. The latest bioperl-run release is


The main bug fixes in this release are:


- OBDA Registry code is up to latest specs and fuly functional
- Sequence retrieval from NCBI  works again after URL change 
- The BLAST output parsed now works on megablast and parses 
  even the last hit
- Result writers now correctly report alignment start/end info
  for translated BLAST/FASTA searches 
- Improvements in closing and keeping open file handles
- Robustness of Bio::Graphics modules have been improved

- Other improved modules:
    o Bio::OntologyIO::dagflat
    o Bio::Annotation::OntologyTerm 
    o Bio::TreeIO::newick
    o Bio::Tools::BPbl2seq
    o Bio::Tools::Genemark
    o Bio::SeqIO::genbank


- SoapLab and PISE improvements
- New wrapper for Vista: http://www-gsd.lbl.gov/vista/
- Other improved modules:
    o Bio::Tools::Run::Eponine
    o Bio::Tools::Run::FootPrinter
    o Bio::Tools::Run::Genewise
    o Bio::Tools::Run::Genscan
    o Bio::Tools::Run::Hmmpfam
    o Bio::Tools::Run::Mdust
    o Bio::Tools::Run::Signalp
    o Bio::Tools::Run::Phylo::Phylip::SeqBoot
    o Bio::Tools::Run::Phylo::Phylip::Neighbor
    o Bio::Tools::Run::Alignment::Blat
    o Bio::Tools::Run::Alignment::Lagan

More details are in distribution file 'Changes'.

Thank you for all who reported bugs and made this release possible.

On behalf of the Bioperl core team,


______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________

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