PatMaN: rapid alignment of short sequences to large databases.
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.


BACKGROUND
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.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Prüfer
Kay
K
Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. pruefer@eva.mpg.de
Stenzel
Udo
U
Dannemann
Michael
M
Green
Richard E
RE
Lachmann
Michael
M
Kelso
Janet
J
D000465:Algorithms; D001483:Base Sequence; D003628:Database Management Systems; D030541:Databases, Genetic; D016247:Information Storage and Retrieval / Q000379:methods*; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software