This tool is designed to solve generalized pattern matching problem, by which we only find a set of sub-patterns, ignoring the gaps in between the sub-patterns. This tool is extremely fast and also has good tolerance to errors.

Features

  • pattern matching in human genome in less than one minute
  • hard-disk based k-mers index
  • complementary dual-seeding
  • pruned DP in extending
  • short seed length k has good tolerance of errors
  • both positive and negative gaps can be handled

Project Activity

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Categories

Bio-Informatics

License

Academic Free License (AFL)

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Generalized Pattern Matching Web Site

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Additional Project Details

Operating Systems

Linux, BSD

Languages

English

Intended Audience

Advanced End Users

User Interface

Command-line

Programming Language

C

Database Environment

Other API

Related Categories

C Bio-Informatics Software

Registered

2010-08-20
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