• Parsing regulatory DNA: General tasks, techniques, and the PhyloGibbs approach

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    • Keywords


      PhyloGibbs; regulatory DNA; transcription factors

    • Abstract


      In this review, we discuss the general problem of understanding transcrip tional regulation from DNA sequence and prior information. The main tasks we discuss are predicting local regions of DNA, cis-regulatory modules (CRMs) that contain binding sites for transcription factors (TFs), and predicting individ ual binding sites. We review various existing methods, and then describe the approach taken by PhyloGibbs, a recent motif-finding algorithm that we developed to predict TF binding sites, and PhyloGibbs-MP, an extension to PhyloGibbs that tackles other tasks in regulatory genomics, particularly prediction of CRMs.

    • Author Affiliations


      Rahul Siddharthan1

      1. The Institute of Mathematical Sciences, Chennai 600 113, India
    • Dates

  • Journal of Biosciences | News

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      Posted on July 25, 2019

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