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Bioinformatics Vol. 17 no. 12 2001
Pages 1234-1235
© 2001 Oxford University Press

Applications Note

mmsearch: a motif arrangement language and search program

Thomas Junier , Marco Pagni and Philipp Bucher

Swiss Institute of Bioinformatics, Switzerland

Received on April 5, 2001 ; revised on June 8, 2001 ; accepted on July 2, 2001

Summary: This paper presents a language for describing arrangements of motifs in biological sequences, and a program that uses the language to find the arrangements in motif match databases. The program does not by itself search for the constituent motifs, and is thus independent of how they are detected, which allows it to use motif match data of various origins.

Availability: The program can be tested online at http://hits.isb-sib.ch and the distribution is available from ftp://ftp.isrec.isb-sib.ch/pub/software/unix/mmsearch-1.0.tar.gz

Contact: Thomas.Junier{at}isrec.unil.ch

Supplementary information: The full documentation about mmsearchis available from http://hits.isb-sib.ch/~tjunier/mmsearch/doc.


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