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Bio-Grep-v0.9.2
River stage zero No dependents

Changes for version 0.9.2 - 2007-08-17

  • POD improvements
  • huge performance improvements (RE, Agrep)
  • support for TRE agrep
  • skip EMBOSS alignment calculation when hits can't have gaps
  • idsonly option in bgrep
  • better exception texts
  • sequence description in RE results
  • benchmarks

Documentation

Bio::Grep::Benchmarks
Bio::Grep Benchmarks
Bio::Grep::Cookbook
Bio::Grep Cookbook
bgrep
Wrapper for several suffix array tools

Modules

Bio::Grep
Perl extension for searching in Fasta files
Bio::Grep::Backend::Agrep
Agrep back-end
Bio::Grep::Backend::BackendI
Superclass for all back-ends
Bio::Grep::Backend::GUUGle
GUUGle back-end
Bio::Grep::Backend::RE
Perl Regular Expression back-end
Bio::Grep::Backend::Vmatch
Vmatch back-end
Bio::Grep::Filter::FilterI
Superclass for all filter modules
Bio::Grep::Filter::FilterRemoveDuplicates
Example Filter
Bio::Grep::Root
Superclass for all Bio::Grep* packages
Bio::Grep::SearchResult
Data structure for a back-end search hit
Bio::Grep::SearchSettings
Data structure for all search settings

Other files