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  • Fast prediction of DNA melting bubbles using DNA thermodynamic stability [Elektronski vir]
    Zrimec, Jan ; Lapanje, Aleš
    DNA melting bubbles are the basis of many DNA-protein interactions, such as those in regulatory DNA regions driving gene expression, DNA replication and bacterial horizontal gene transfer. Bubble ... formation is affected by DNA duplex stability and thermally induced duplex destabilization (TIDD). Although prediction of duplex stability with the nearest neighbor (NN) method is much faster than prediction of TIDD with the Peyrard-Bishop-Dauxois (PBD) model, PBD predicted TIDD defines regulatory DNA regions with higher accuracy and detail. Here, we considered that PBD predicted TIDD is inherently related to the intrinsic duplex stabilities of destabilization regions. We show by regression modeling that NN duplex stabilities can be used to predict TIDD almost as accurately as is predicted with PBD. Predicted TIDD is in fact ascribed to non-linear transformation of NN duplex stabilities in destabilization regions as well as effects of neighboring regions relative to destabilization size. Since the prediction time of our models is over 6 orders of magnitude shorter than that of PBD, the models present an accessible tool for researchers. TIDD can be predicted on our webserver at tidd.immt.eu.
    Vir: IEEE/ACM transactions on computational biology and bioinformatics. - ISSN 1545-5963 (Vol. 12, iss. 5, 2015, str. 1137-1145)
    Vrsta gradiva - e-članek ; neleposlovje za odrasle
    Leto - 2015
    Jezik - angleški
    COBISS.SI-ID - 37766405

    Povezava(-e):

    http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=8857
    DOI

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