PatMaN: rapid alignment of short sequences to large databases.

by: Kay Prüfer, Udo Stenzel, Michael Dannemann, Richard E E Green, Michael Lachmann, Janet Kelso

Bioinformatics (Oxford, England) (8 May 2008)

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Abstract

SUMMARY: We present a tool suited for searching for many short nucleotide sequences in large databases, allowing for a pre-defined number of gaps and mismatches. The commandline-driven program implements a nondeterministic 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. CONTACT: pruefer@eva.mpg.de.

@article{citeulike:2803684, abstract = {SUMMARY: We present a tool suited for searching for many short nucleotide sequences in large databases, allowing for a pre-defined number of gaps and mismatches. The commandline-driven program implements a nondeterministic 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. CONTACT: pruefer@eva.mpg.de.}, address = {Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.}, author = {Pr\"{u}fer, Kay and Stenzel, Udo and Dannemann, Michael and Green, Richard E E. and Lachmann, Michael and Kelso, Janet }, citeulike-article-id = {2803684}, doi = {10.1093/bioinformatics/btn223}, issn = {1460-2059}, journal = {Bioinformatics (Oxford, England)}, keywords = {alignment}, month = {May}, posted-at = {2008-05-16 03:44:38}, priority = {2}, title = {PatMaN: rapid alignment of short sequences to large databases.}, url = {http://dx.doi.org/10.1093/bioinformatics/btn223}, year = {2008} }

RIS record

TY - JOUR ID - citeulike:2803684 L3 - citeulike-article-id:2803684 TI - PatMaN: rapid alignment of short sequences to large databases. JF - Bioinformatics (Oxford, England) AD - Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. SN - 1460-2059 N2 - SUMMARY: We present a tool suited for searching for many short nucleotide sequences in large databases, allowing for a pre-defined number of gaps and mismatches. The commandline-driven program implements a nondeterministic 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. CONTACT: pruefer@eva.mpg.de. KW - alignment AU - Prüfer, Kay AU - Stenzel, Udo AU - Dannemann, Michael AU - Green, Richard E AU - Lachmann, Michael AU - Kelso, Janet PY - 2008/05/08/ UR - http://dx.doi.org/10.1093/bioinformatics/btn223 ER -

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