Significance Assessment of the Difference in MAtrix MAtches

SADMAMA is designed to address the question of whether one set of sequences has more and/or better binding sites of a particular transcription factor than the other. The binding sites are modeled as matches to a position weight matrix (PWM) which is presumed to be known.

For more details please refer to the paper.

You can download the C source code of the version that was used for the tests mentioned in the paper here. There's a newer version that should be made available soon with some bug fixes and some new features.

If SADMAMA helps your research you can cite it as:

Uri Keich, Hong Gao, Jeffrey S Garretson, Anand Bhaskar, Ivan Liachko, Justin Donato and Bik K Tye.
Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast. BMC Bioinformatics 2008, 9:372.