Bio::Grep - Perl extension for searching in DNA and Protein sequences River stage zero No dependents

Bio-Grep is a collection of Perl modules for searching in DNA and Protein sequences. It supports different back-ends, most importantly some (enhanced) suffix array implementations. Currently, there is no suffix array tool that works in all scenarios ...

LIMAONE/Bio-Grep-v0.10.6 - 12 Nov 2009 20:01:33 UTC

Bio::Grep::Root - Superclass for all Bio::Grep* packages River stage zero No dependents

This superclass adds some useful methods to all Bio::Grep packages....

LIMAONE/Bio-Grep-v0.10.6 - 12 Nov 2009 20:01:33 UTC

Bio::Grep::Cookbook - Bio::Grep Cookbook River stage zero No dependents

This collection of recipes intends to provide you solutions for the most common problems and to make the development process easier....

LIMAONE/Bio-Grep-v0.10.6 - 12 Nov 2009 20:01:33 UTC

Bio::Grep::Benchmarks - Bio::Grep Benchmarks River stage zero No dependents

A collection of quick and dirty benchmarks....

LIMAONE/Bio-Grep-v0.10.6 - 12 Nov 2009 20:01:33 UTC

Bio::Grep::Backend::RE - Perl Regular Expression back-end River stage zero No dependents

Bio::Grep::Backend::RE searches for a query with a Perl Regular Expression. Internally, it pre-compiles the specified regex (with the appended modifiers i, m, s and x), matches it against every line in the database with the looping modifier g, and th...

LIMAONE/Bio-Grep-v0.10.6 - 12 Nov 2009 20:01:33 UTC

Bio::Grep::SearchResult - Data structure for a back-end search hit River stage zero No dependents

Bio::Grep::SearchResult is the data structure for one hit in the database....

LIMAONE/Bio-Grep-v0.10.6 - 12 Nov 2009 20:01:33 UTC

Bio::Grep::Backend::Agrep - Agrep back-end River stage zero No dependents

Bio::Grep::Backend::Agrep searches for a query with agrep....

LIMAONE/Bio-Grep-v0.10.6 - 12 Nov 2009 20:01:33 UTC

Bio::Grep::SearchSettings - Data structure for all search settings River stage zero No dependents

Bio::Grep::SearchSettings is the data structure for all search settings. Not all back-ends will support every option....

LIMAONE/Bio-Grep-v0.10.6 - 12 Nov 2009 20:01:33 UTC

Bio::Grep::Backend::Vmatch - Vmatch back-end River stage zero No dependents

Bio::Grep::Backend::Vmatch searches for a query in a "Vmatch" suffix array....

LIMAONE/Bio-Grep-v0.10.6 - 12 Nov 2009 20:01:33 UTC

Bio::Grep::Filter::FilterI - Superclass for all filter modules River stage zero No dependents

Bio::Grep::Filter::FilterI is the superclass for all filter modules. Don't use this directly. A Filter module implements a filter function that returns 1 if query and subject pass the filter, 0 otherwise. If the member variable "delete" is 1, then th...

LIMAONE/Bio-Grep-v0.10.6 - 12 Nov 2009 20:01:33 UTC

Bio::Grep::Backend::GUUGle - GUUGle back-end River stage zero No dependents

Bio::Grep::Backend::GUUGle searches for a query in a "GUUGle" suffix array....

LIMAONE/Bio-Grep-v0.10.6 - 12 Nov 2009 20:01:33 UTC

Bio::Grep::Backend::BackendI - Superclass for all back-ends River stage zero No dependents

Bio::Grep::Backend::BackendI is the superclass for all back-ends. Don't use this class directly....

LIMAONE/Bio-Grep-v0.10.6 - 12 Nov 2009 20:01:33 UTC

Bio::Grep::Filter::FilterRemoveDuplicates - Example Filter River stage zero No dependents

Bio::Grep::Filter::FilterRemoveDuplicates is an example filter that allows only unique sequence ids in search results. It is useful if you are only interested in which genes the query was found. Deletes the result if the id already occurred. Ignores ...

LIMAONE/Bio-Grep-v0.10.6 - 12 Nov 2009 20:01:33 UTC

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