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Bioinformatics. 2008 Jul 1;24(13):1530-1. doi: 10.1093/bioinformatics/btn223. Epub 2008 May 8.

PatMaN: rapid alignment of short sequences to large databases.

Author information

1
Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. pruefer@eva.mpg.de

Abstract

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 http://bioinf.eva.mpg.de/patman.

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
18467344
PMCID:
PMC2718670
DOI:
10.1093/bioinformatics/btn223
[Indexed for MEDLINE]
Free PMC Article
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