title: mmsearch: a motif arrangement language and search program.
abstract: 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.
  
  
  BACKGROUND
  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
  
  
  BACKGROUND
  Thomas.Junier@isrec.unil.ch
  
  
  BACKGROUND
  The full documentation about mmsearchis available from http://hits.isb-sib.ch/~tjunier/mmsearch/doc.
authors.affiliation: Swiss Institute of Bioinformatics, Switzerland. Thomas.Junier@isrec.unil.ch
authors.forename: T
authors.initials: T
authors.lastname: Junier
authors.forename: M
authors.initials: M
authors.lastname: Pagni
authors.forename: P
authors.initials: P
authors.lastname: Bucher
mesh_terms: D011381:Programming Languages; D011506:Proteins / Q000032:analysis*; D018121:Receptors, Cytokine / Q000032:analysis; D012984:Software; D013879:Thioredoxins / Q000032:analysis
chemical_list: D011506:Proteins; D018121:Receptors, Cytokine; D013879:Thioredoxins