title: iMotifs: an integrated sequence motif visualization and analysis environment.
abstract: BACKGROUND
  Short sequence motifs are an important class of models in molecular biology, used most commonly for describing transcription factor binding site specificity patterns. High-throughput methods have been recently developed for detecting regulatory factor binding sites in vivo and in vitro and consequently high-quality binding site motif data are becoming available for increasing number of organisms and regulatory factors. Development of intuitive tools for the study of sequence motifs is therefore important. iMotifs is a graphical motif analysis environment that allows visualization of annotated sequence motifs and scored motif hits in sequences. It also offers motif inference with the sensitive NestedMICA algorithm, as well as overrepresentation and pairwise motif matching capabilities. All of the analysis functionality is provided without the need to convert between file formats or learn different command line interfaces. The application includes a bundled and graphically integrated version of the NestedMICA motif inference suite that has no outside dependencies. Problems associated with local deployment of software are therefore avoided.
  
  
  BACKGROUND
  iMotifs is licensed with the GNU Lesser General Public License v2.0 (LGPL 2.0). The software and its source is available at http://wiki.github.com/mz2/imotifs and can be run on Mac OS X Leopard (Intel/PowerPC). We also provide a cross-platform (Linux, OS X, Windows) LGPL 2.0 licensed library libxms for the Perl, Ruby, R and Objective-C programming languages for input and output of XMS formatted annotated sequence motif set files.
  
  
  BACKGROUND
  matias.piipari@gmail.com; imotifs@googlegroups.com.
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK. matias.piipari@gmail.com
authors.forename: Matias
authors.initials: M
authors.lastname: Piipari
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Down
authors.forename: Harpreet
authors.initials: H
authors.lastname: Saini
authors.forename: Anton
authors.initials: A
authors.lastname: Enright
authors.forename: Tim J P
authors.initials: TJ
authors.lastname: Hubbard
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface