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A lot of changes have been made to the BioRuby 1.4.2 after the version 1.4.1 is released. This document describes important and/or incompatible changes since the BioRuby 1.4.1 release.

For known problems, see KNOWN_ISSUES.rdoc.

New features

Speed-up of Bio::RestrictionEnzyme::Analysis.cut

The running speed of Bio::RestrictionEnzyme::Analysis.cut is significantly increased. The new code is 50 to 80 fold faster than the previous code when cutting 1Mbp sequence running on Ruby 1.9.2p180. The code is written by Tomoaki NISHIYAMA and Naohisa Goto.

Tutorial is updated

The Tutorial.rd is updated by Pjotr Prins and Michael O'Keefe.

Many unit tests are added

Added many unit tests for Bio::GenBank, Bio::GenPept, Bio::NBRF, Bio::PDB and so on. They are developed by Kazuhiro Hayashi during the Google Summer of Code 2010.

Other new features

  • In GenomeNet remote BLAST execution, support for database “mine-aa” and “mine-nt” with KEGG organism codes is added.

  • Support for Ruby 1.9.2 is improved.

Bug fixes


  • Failure of remote BLAST execution is fixed, due to the changes in GenomeNet and DDBJ.

  • When executing remote BLAST with “genomenet” server, options “-b” and “-v” are now correctly used to limit the number of hits to be reported.

Other bug fixes

  • Bio::Reference#pubmed_url is updated to follow recent NCBI changes.

  • Fixed: Bio::Newick#reparse failure.

  • Fixed: In Bio::MEDLINE#reference, doi field should be filled.

  • Fixed: Bio::Reference#endnote fails when url is not set.

  • Fixed: Bio::FastaFormat#query passes nil to the given factory object.

Incompatible changes

Bio::Blast with the remote GenomeNet server

When executing remote BLAST with “genomenet” server, options “-b” and “-v” are now correctly used to limit the number of hits to be reported. In 1.4.1 and before, “-B” and “-V” were mistakenly used for the purpose.

Bio::RestrictionEnzyme internal data structure

Due to the speedup, internal data structure of the following classes are changed: Bio::RestrictionEnzyme::Range::SequenceRange, Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts, Bio::RestrictionEnzyme::Range::SequenceRange::Fragment. This indicates that Marshal.dump (and YAML.dump) data generated by older versions cannot be loaded by the new version, and vice versa, although public APIs of the classes keep compatibility.

Known issues

The following issues are added or updated. See KNOWN_ISSUES.rdoc for other already known issues.

(to be written)

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