A Flexible Motif Search Technique Based on Generalized Prooles

Draft Copy|January 24, 1996|Do not circulate. 0 abstract A exible motif search technique is presented which has two major components: 1. a generalized proole syntax serving as a motif deenition language 2. a motif search method speciically adapted to the problem of nding multiple instances of a motif in the same sequence. The new proole structure, which is the core of the generalized proole syntax, combines the functions of a variety of motif descriptors implemented in other methods, including regular expression-like patterns, weight matrices, previously used prooles, and certain types of hidden Markov models (hmms). The relationship between generalized prooles and other biomolecular motif descriptors is analyzed in detail, with special attention to hmms. Generalized prooles are shown to be equivalent to a particular class of hmms, and conversion procedures in both directions are given. The conversion procedures provide an interpretation for local alignment in the framework of stochastic models, allowing for clear, simple signiicance tests. A mathematical statement of the motif search problem deenes the new method exactly without linking it to a speciic algorithmic solution. Part of the deenition includes a new deenition of disjointness of alignments. Draft Copy|January 24, 1996|Do not circulate.