PatMaN: rapid alignment of short sequences to large databases. Summary: We present a tool suited for searching for many short nucleotide sequences in large databases, allowing for a predefined number of gaps and mismatches. The commandline-driven program implements a non-deterministic automata matching algorithm on a keyword tree of the search strings. Both queries with and without ambiguity codes can be searched. Search time is short for perfect matches, and retrieval time rises exponentially with the number of edits allowed. Availability: The C++ source code for PatMaN is distributed under the GNU General Public License and has been tested on the GNU/Linux operating system. It is available from

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References in zbMATH (referenced in 4 articles )

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  1. Rodríguez-Ezpeleta, Naiara (ed.); Hackenberg, Michael (ed.); Aransay, Ana M. (ed.): Bioinformatics for high throughput sequencing (2012)
  2. Saeed, Fahad; Perez-Rathke, Alan; Gwarnicki, Jaroslaw; Berger-Wolf, Tanya; Khokhar, Ashfaq: A high performance multiple sequence alignment system for pyrosequencing reads from multiple reference genomes (2012) ioport
  3. Noé, Laurent; Gîrdea, Marta; Kucherov, Gregory: Designing efficient spaced seeds for SOLiD read mapping (2010)
  4. Prüfer, Kay; Stenzel, Udo; Dannemann, Michael; Green, Richard E.; Lachmann, Michael; Kelso, Janet: Patman: Rapid alignment of short sequences to large databases. (2008) ioport