Tmod is developed for the users of
Windows operating systems, and has an easy-to-use graphical user
interface (GUI). Tmod integrates twelve motif discovery programs:
AlignACE (Roth et al., 1998), BioProspector (Liu et al., 2001),
Consensus (Hertz and Stormo, 1999), MEME (Bailey and Elkan, 1994),
MDscan (Liu et al., 2002), MotifSampler(Thijs, et al., 2001; Thijs,
et al., 2002), SeSiMCMC (Favorov, et al., 2005), GLAM (Frith, et
al., 2004), MotifRegressor(Conlon, et al., 2003), YMF(Sinha and
Tompa, 2003), Weeder (Pavesi, et al., 2001; Pavesi, et al., 2004;
Pavesi, et al., 2004) and Gibbs Motif Sampler (Liu, et al., 1995;
Newberg, et al., 2007; Thompson, et al., 2004; Thompson, et al.,
2003; Thompson, et al., 2007). The motif finding algorithms included
in Tmod have all been widely cited and proved excellent methods in
the research field of motif discovery.
Tmod is developed in C++ with the support of MFC and Cygwin. and compiled on Windows platform and can be executed on Windows 7/Windows Vista/Windows XP/Windows 2000 system. The minimum memory (RAM) requirement of Tmod is 256MB.
Tmod 1.1.1 can be downloaded from here.
Download Tmod.rar. Unzip the file to anywhere on your computer by Winrar. The installation is OK.
(1) To get the best visual effect, we recommend to set the screen resolution at 1280*1024 or higher.
(2) If software Cygwin has already been installed on your computer, you may encounter some conflicts. You should get the cygwin1.dll from C:\cygwin\bin, and replace all the files named “cygwin1.dll” under the Tmod root directory and subdirectories.
The user's manual can be downloaded from here.
For MotifRegressor, we changed its main Perl script into an executable program, and rewrote the stepwise regression part in Matlab and compiled the M file to an executable file. After these modifications, MotifRegressor can run well on the Windows platform without S-PLUS.
To run MotifRegressor, MATLAB Component Runtime (MCRInstaller) is needed. MCRInstaller 7.8 (227MB) can be downloaded from here.
The source code of Tmod can be obtained from the authors.
If you use Tmod, please cite our paper: Hanchang Sun, Yuan Yuan, Yibo Wu, Hui Liu, Jun S. Liu and Hongwei Xie. Tmod: Toolbox of Motif Discovery. Bioinformatics, 2010, 26(3): 405-407. The paper can be downloaded from here.
The CRP result files can be downloaded from here.
Prof. Hongwei Xie
Prof. Jun S. Liu