Hidden Markov Models for Human Genes: Periodic Patterns in Exon Sequences

Pierre Baldi, Søren Brunak, Yves Chauvin, Anders Stærmose Krogh

    Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

    Abstract

    We analyse the sequential structure of human genomic DNA by hidden Markov models. We apply models of widely different design: conventional left-right constructs and models with a built-in periodic architecture. The models are trained on segments of DNA sequences extracted such that they cover complete internal exons flanked by introns, or splice sites flanked by coding and non-coding sequence. Together, models of donor site regions, acceptor site regions and flanked internal exons, show that exons - besides the reading frame - hold a specific periodic pattern. The pattern has the consensus: non-T(A/T)G and a minimal periodicity of roughly 10 nucleotides.
    Original languageEnglish
    Title of host publicationTheoretical and Computational Methods in Genome Research
    Place of PublicationNew York
    PublisherPlenum Publishing Corporation
    Publication date1997
    Pages15-32
    ISBN (Print)0-306-45503-X
    Publication statusPublished - 1997
    EventInternational Symposium on Theoretical and Computational Genome Research - Heidelberg, Germany
    Duration: 24 Mar 199627 Mar 1996

    Conference

    ConferenceInternational Symposium on Theoretical and Computational Genome Research
    CountryGermany
    CityHeidelberg
    Period24/03/199627/03/1996

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