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Bioperl-1.2.1 includes bug fixes for standaloneblast and bio::coordinate, indicating improvements in sequencing tools.
The release is available at http://www.bioperl.org/ftp/DIST/bioperl-1.2.1.tar.gz and is propagating around CPAN now. The main bug fixes in this release are: - inclusion of WrapperBase, making StandAloneBlast work from the release - fixes and cleanup of Bio::Coordinate - fixes to Bio::Index::EMBL and bpindex The 1.2.1 release does see some major additions in the Ontology area.
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A 2003 study studied this question.
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