We found a match
Your institution may have rights to this item. Sign in to continue.
- Title
PatMaN: rapid alignment of short sequences to large databases.
- Authors
Kay Prüfer; Udo Stenzel; Michael Dannemann; Richard E. Green; Michael Lachmann; Janet Kelso
- Abstract
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 http://bioinf.eva.mpg.de/patman. Contact: pruefer@eva.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online.
- Subjects
NUCLEOTIDE analysis; NUCLEOTIDE sequence; COMPUTERS in medicine; COMPUTER software
- Publication
Bioinformatics, 2008, Vol 24, Issue 13, p1530
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btn223