About Tmod

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 download and installation


Download:

Tmod 1.1.1 can be downloaded from here.

 

Installation:

Download Tmod.rar. Unzip the file to anywhere on your computer by Winrar. The installation is OK.

Notice:

(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.

 

User's manual:

The user's manual can be downloaded from here.

 

MCRInstaller:

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.

 

Source code:

The source code of Tmod can be obtained from the authors.

 

Tmod paper:

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.


 

CRP results

 

The CRP result files can be downloaded from here.


Contact us

 

Prof. Hongwei Xie

E-mail: xhwei65@nudt.edu.cn

 

 

Prof. Jun  S. Liu

E-mail: jliu@stat.harvard.edu

 

 

Hanchang Sun

E-mail: sunhc@nudt.edu.cn