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Background  In analyzing the stability of DNA replication origins in  Saccharomyces cerevisiae  we faced the question whether one set of sequences is significantly enriched in the number and/or the quality of the matches of a particular position weight matrix relative to another set.    Results  We present SADMAMA, a computational solution to a address this problem. SADMAMA implements two types of statistical tests to answer this question: one type is based on simplified models, while the other relies on bootstrapping, and as such might be preferable to users who are averse to such models. The bootstrap approach incorporates a novel "site-protected" resampling procedure which solves a problem we identify with naive resampling.    Conclusion  SADMAMA's utility is demonstrated here by offering a plausible explanation to the differential ARS activity observed in our previous  mcm1-1  mutant experiments [ 1 ], by suggesting the relevance of multiple weak ACS matches to efficient replication origin function in  Saccharomyces cerevisiae , and by suggesting an explanation to the observed negative effect  FKH2  has on chromatin silencing [ 2 ]. SADMAMA is available for download from   .

bmc bioinformatics

Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast