EMBOSS

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EMBOSS -- European Molecular Biology Open Software Suite -- is a free open source software analysis package specially developed for the needs of the molecular biology and bioinformatics community [1].

See also the related GCG suite and the Wikipedia EMBOSS article. A list of equivalent tools in EMBOSS to those found in GCG.

Contents

Running EMBOSS programs

The Bio::Factory::EMBOSS module is a generic interface to EMBOSS applications for local running of the tools. Remote interfaces to EMBOSS are available through the PISE interface and the Bio::Tools::Run::AnalysisFactory::Pise module.

est2genome

This tool provides spliced EST to Genome alignments so that alignments account for splice-sites when constructing an alignment and has an explict model for gap insertions at likely splice-sites. Is part of EMBOSS, but see the EST2genome page for more information.

Perl and EMBOSS (outside of BioPerl)

XS-based Perl modules that interacts with the EMBOSS packages exist which are not directly related to BioPerl (Bio::Emboss). Not much is known about them, but they appear to be regularly maintained.

References

  1. Rice P, Longden I, and Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. PubMed ID:10827456 | HubMed [emboss]
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