PatMaN -- a DNA pattern matcher for short sequences
What you can do:
Rapid alignment of short sequences to large databases.
Highlights:
- 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.
Keywords:
- short DNA pattern
- DNA motif
- pattern matching
- short nucleotide sequence
Literature & Tutorials:
This record last updated: 08-05-2008