title: Tmod: toolbox of motif discovery.
abstract: CONCLUSIONS
  Motif discovery is an important topic in computational transcriptional regulation studies. In the past decade, many researchers have contributed to the field and many de novo motif-finding tools have been developed, each may have a different strength. However, most of these tools do not have a user-friendly interface and their results are not easily comparable. We present a software called Toolbox of Motif Discovery (Tmod) for Windows operating systems. The current version of Tmod integrates 12 widely used motif discovery programs: MDscan, BioProspector, AlignACE, Gibbs Motif Sampler, MEME, CONSENSUS, MotifRegressor, GLAM, MotifSampler, SeSiMCMC, Weeder and YMF. Tmod provides a unified interface to ease the use of these programs and help users to understand the tuning parameters. It allows plug-in motif-finding programs to run either separately or in a batch mode with predetermined parameters, and provides a summary comprising of outputs from multiple programs. Tmod is developed in C++ with the support of Microsoft Foundation Classes and Cygwin. Tmod can also be easily expanded to include future algorithms.
  
  
  BACKGROUND
  Tmod is available for download at http://www.fas.harvard.edu/~junliu/Tmod/.
authors.affiliation: Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073, China.
authors.forename: Hanchang
authors.initials: H
authors.lastname: Sun
authors.forename: Yuan
authors.initials: Y
authors.lastname: Yuan
authors.forename: Yibo
authors.initials: Y
authors.lastname: Wu
authors.forename: Hui
authors.initials: H
authors.lastname: Liu
authors.forename: Jun S
authors.initials: JS
authors.lastname: Liu
authors.forename: Hongwei
authors.initials: H
authors.lastname: Xie
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D019295:Computational Biology / Q000379:methods*; D017422:Sequence Analysis, DNA; D020539:Sequence Analysis, Protein; D017423:Sequence Analysis, RNA; D012984:Software