Fast approximate motif statistics.
We present in this article a fast approximate method for computing the statistics of a number of non-self-overlapping matches of motifs in a random text in the nonuniform Bernoulli model. This method is well suited for protein motifs where the probability of self-overlap of motifs is small. For 96% of the PROSITE motifs, the expectations of occurrences of the motifs in a 7-million-amino-acids random database are computed by the approximate method with less than 1% error when compared with the exact method. Processing of the whole PROSITE takes about 30 seconds with the approximate method. We apply this new method to a comparison of the C. elegans and S. cerevisiae proteomes.
Nicodème
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DKFZ Theoretische Bioinformatik, 69120 Heidelberg, Germany. nicodeme@genopole.cnrs.fr
D020816:Amino Acid Motifs; D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics; D016208:Databases, Factual; D016678:Genome; D015233:Models, Statistical; D016012:Poisson Distribution; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012984:Software