PhyME: A Software Tool for Finding Motifs in Sets of Orthologous Sequences

Research output: Chapter in Book/Report/Conference proceedingChapter


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.

Original languageEnglish (US)
Title of host publicationMotif finding multiple species evolutionary tree expectation maximization
EditorsNicholas H Bergman
PublisherHumana Press
Number of pages10
ISBN (Electronic)978-1-59745-514-5
ISBN (Print)978-1-58829-693-1, 978-1-61737-722-8
StatePublished - 2007

Publication series

Name Methods in Molecular Biology
PublisherHumana Press
ISSN (Print)1064-3745


  • Algorithms
  • Binding Sites
  • Biological Evolution
  • Sequence Alignment
  • Software
  • Transcription Factors/metabolism


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