MultiModule: Discovery of cis-regulatory modules in multiple species by coupling hidden Markov models

Related paper:

Zhou, Q. and Wong, W.H. (2007). Coupling hidden Markov models for the discovery of cis-regulatory modules in multiple species. The Annals of Applied Statistics, 1: 36-65.

Supplemental Notes.

Data sets in the paper

Muscle-specific genes in human, mouse and dog orthologs: sequences and known TFBS's.
Early developmental genes in drosophila orthologs: sequences and known TFBS's.

Download MultiModule (beta v.1, Nov, 2007)

Please download the MultiMod.tar file for the package of MultiModule. Put this tar file in a Linux or OS directory and use "tar xvf MultiModule.tar" to unpack the file. Then you will find the following files:

1. MultiModuleU (Linux executable).
2. MultiModuleOS (OS executable).
3. Readme.pdf: A user manual, including the input sequence format, the usage of options, etc.
4. InputSeq.fa: An example input data set for MultiModule.
5. The typical command to run MultiModule on InputSeq.fa.
6. Output_results.txt: An expected output file of the example data set from MultiModule.
7. Other output files: See Readme.pdf for more details.

You may also type "./MultiModuleOS" or "./MultiModuleU" for a simple manual on input options. Please run repeat masker before using MultiModule.

Link to a related program that discovers cis-regulatory modules in single species data: CisModule.