PatMaN: rapid alignment of short sequences to large databases.
other · Level V
Where this comes from
- Record sourced from PubMed, PMID 18467344.
- Also identified by DOI 10.1093/bioinformatics/btn223 and PMC identifier 2718670.
- Licence recorded as CC BY-NC.
- Because redistribution is not established, this page shows the abstract only. Follow the links below for the full text.
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. 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 data are available at Bioinformatics online.
Medical subject headings
- Algorithms
- Database Management Systems
- Databases, Genetic
- Information Storage and Retrieval
- Sequence Alignment
- Sequence Analysis, DNA
- Software