PatMaN: rapid alignment of short sequences to large databases

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 que...

Descripción completa

Detalles Bibliográficos
Autores principales: Prüfer, Kay, Stenzel, Udo, Dannemann, Michael, Green, Richard E., Lachmann, Michael, Kelso, Janet
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2008
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718670/
https://www.ncbi.nlm.nih.gov/pubmed/18467344
http://dx.doi.org/10.1093/bioinformatics/btn223
Descripción
Sumario: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.

Ejemplares similares