CisModScan: Scanning for cis-regulatory modules with given motif patterns

Related papers:
1) Johnson, D.S., Zhou, Q., Yagi, K., Satoh, N., Wong, W.H., and Sidow, A. (2005). De dovo discovery of a tissue-specific gene regulatory module in a chordate. Genome Research, 15: 1315-1324.
2) Zhou, Q. and Wong, W.H. (2004). CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling. Proceedings of the National Academy of Sciences USA, 101: 12114-12119.

Download CisModScan programs.

Please download the readme file for this program with a test data set (including an example file for input weight matrices).

1. CisModScanU (Linux executable).
Put this tar file in a Linux directory and use "tar xvf CisModScanU.tar" to unpack the file. Then type "./CisModScanU" for user manual.
The latest update was performed on Aug. 17, 2005.

2. CisModScanOS (OS executable).
Put this tar file in an OS directory and use "tar xvf CisModScanOS.tar" to unpack the file. Then type "./CisModScanOS" for user manual.
The latest update was performed on Aug. 17, 2005.

3. CisModScanW (Windows executable).
The latest update was performed on Aug. 17, 2005.

If you cannot run the above program in your system, your may compile an executable version from the c++ source code by "g++ *.cpp -lm -o CisModScan -O3".

Please run repeat masker before using CisModScan.

Link to a related de novo module discovery program: CisModule.