{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,21]],"date-time":"2025-05-21T16:27:38Z","timestamp":1747844858926},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Availability: Tmod is available for download at http:\/\/www.fas.harvard.edu\/\u223cjunliu\/Tmod\/<\/jats:p>\n               <jats:p>Contact: \u00a0xhwei65@nudt.edu.cn; jliu@stat.harvard.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp681","type":"journal-article","created":{"date-parts":[[2009,12,11]],"date-time":"2009-12-11T01:51:16Z","timestamp":1260496276000},"page":"405-407","source":"Crossref","is-referenced-by-count":18,"title":["Tmod: toolbox of motif discovery"],"prefix":"10.1093","volume":"26","author":[{"given":"Hanchang","family":"Sun","sequence":"first","affiliation":[{"name":"1 Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073, China and 2 Department of Statistics, Harvard University, Cambridge, MA 02138-2931, USA"}]},{"given":"Yuan","family":"Yuan","sequence":"additional","affiliation":[{"name":"1 Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073, China and 2 Department of Statistics, Harvard University, Cambridge, MA 02138-2931, USA"}]},{"given":"Yibo","family":"Wu","sequence":"additional","affiliation":[{"name":"1 Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073, China and 2 Department of Statistics, Harvard University, Cambridge, MA 02138-2931, USA"}]},{"given":"Hui","family":"Liu","sequence":"additional","affiliation":[{"name":"1 Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073, China and 2 Department of Statistics, Harvard University, Cambridge, MA 02138-2931, USA"}]},{"given":"Jun S.","family":"Liu","sequence":"additional","affiliation":[{"name":"1 Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073, China and 2 Department of Statistics, Harvard University, Cambridge, MA 02138-2931, USA"}]},{"given":"Hongwei","family":"Xie","sequence":"additional","affiliation":[{"name":"1 Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073, China and 2 Department of Statistics, Harvard University, Cambridge, MA 02138-2931, USA"}]}],"member":"286","published-online":{"date-parts":[[2009,12,10]]},"reference":[{"key":"2023012511003192100_B1","first-page":"28","article-title":"Fitting a mixture model by expectation maximization to discover motifs in biopolymers","volume":"2","author":"Bailey","year":"1994","journal-title":"Proc. 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