SADMAMA (Significance Assessment of the Difference in MAtrix MAtches / SM) was originally 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, possibly gapped, position weight matrix (PWM) which is presumed to be known.
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Uri Keich et al.
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 doi:10.1186/1471-2105-9-372