PatMaN

The tool PatMaN is a command-line program that can search for many short nucleotide sequences in large databases with predefined gaps and mismatches. It uses a non-deterministic automata matching algorithm on a keyword tree of the search strings, allowing for searches with and without ambiguity codes. The program has been tested on the GNU/Linux operating system.

Topic

Mapping;Genomics;Bioinformatics

Detail

  • Operation: Multiple sequence alignment;Global alignment;Read mapping;Data retrieval

  • Software interface: Command-line user interface

  • Language: C++

  • License: -

  • Cost: Free

  • Version name: 1.2.2

  • Credit: The Max-Planck Society.

  • Input: -

  • Output: -

  • Contact: Kay Prüfer pruefer@eva.mpg.de, Udo Stenzel udo_stenzel@eva.mpg.de

  • Collection: -

  • Maturity: -

Publications

  • PatMaN: rapid alignment of short sequences to large databases.
  • Prüfer K, et al. PatMaN: rapid alignment of short sequences to large databases. PatMaN: rapid alignment of short sequences to large databases. 2008; 24:1530-1. doi: 10.1093/bioinformatics/btn223
  • https://doi.org/10.1093/bioinformatics/btn223
  • PMID: 18467344
  • PMC: PMC2718670

Download and documentation

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