Waiting times for clumps of patterns and for structured motifs in random sequences

Valeri Stefanov, S. Robin, S. Schbath

    Research output: Contribution to journalArticle

    14 Citations (Scopus)

    Abstract

    This paper provides exact probability results for waiting times associated with occurrences of two types of motifs in a random sequence. First, we provide an explicit expression for the probability generating function of the interarrival time between two clumps of a pattern. It allows, in particular, to measure the quality of the Poisson approximation which is currently used for evaluation of the distribution of the number of clumps of a pattern. Second, we provide explicit expressions for the probability generating functions of both the waiting time until the first occurrence, and the interarrival time between consecutive occurrences, of a structured motif. Distributional results for structured motifs are of interest in genome analysis because such motifs are promoter candidates. As ail application. we determine significant structured motifs in a data set of DNA regulatory sequences. (c) 2006 Elsevier B.V. All rights reserved.
    Original languageEnglish
    Pages (from-to)868-880
    JournalDiscrete Applied Mathematics
    Volume155
    Issue number6-7
    DOIs
    Publication statusPublished - 2007

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