Sun, H.Yuan, Y.Wu, Y.Liu, H.Liu, JunXie, H.2017-08-072009Sun, H., Y. Yuan, Y. Wu, H. Liu, J. S. Liu, and H. Xie. 2009. “Tmod: Toolbox of Motif Discovery.” Bioinformatics 26, no. 3: 405–407. doi:10.1093/bioinformatics/btp681.1367-4803http://nrs.harvard.edu/urn-3:HUL.InstRepos:33719948Motif 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.en-USJournal Article10.1093/bioinformatics/btp681