Comparative Genomics

Volume 395 of the series Methods in Molecular Biology™ pp 309-317


A Software tool for Finding Motifs in Sets of Orthologous Sequences
  • Saurabh SinhaAffiliated withDepartment of Computer Science, University of Illinois

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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