Tmod: toolbox of motif discovery

Abstract

Summary: 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.

Availability: Tmod is available for download at http://www.fas.harvard.edu/~junliu/Tmod/.

Fig. 1.

Software architecture of the Tmod system. Names displayed at the second level, such as AlignACE, BioProspector, etc., correspond to different motif discovery programs. Each program receives input sequences and parameters through the human–machine interface of Tmod. The motifs found by the programs can be compared using BioOptimizer.

Fig. 2.

(A) The main interface of Tmod. (B) The summary file of consensus sequences parsed from the output files of each program. (C) The summary file of motif information parsed from BioOptimizer sum files.