A Software tool for Finding Motifs in Sets of Orthologous Sequences
  • Saurabh Sinha
Part of the Methods in Molecular Biology™ book series (MIMB, volume 395)


Discovery of transcription factor binding sites is a crucial and challenging problem in bioinformatics. Several computational tools have been developed for this problem, popularly known as the motif-finding problem. PhyME is an ab initio motif-finding algorithm, which finds overrepresented motifs in input sequences while accounting for their evolutionary conservation in orthologs of those sequences. Here, we describe the usage of this algorithm, publicly available as a Linux-based implementation.


Motif finding multiple species evolutionary tree expectation maximization 


  1. 1.
    Sinha, S., Blanchette, M., and Tompa, M. (2004) PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinformatics 5, 170.CrossRefPubMedGoogle Scholar

Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  • Saurabh Sinha
    • 1
  1. 1.Department of Computer ScienceUniversity of Illinois

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