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 publicationComparative Genomics
Subtitle of host publicationVolume 1
EditorsBergman H. Nicholas
Number of pages9
StatePublished - Jan 11 2007
Externally publishedYes

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • Evolutionary tree
  • Expectation maximization
  • Motif finding
  • Multiple species

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


Dive into the research topics of 'PhyME: A software tool for finding motifs in sets of orthologous sequences'. Together they form a unique fingerprint.

Cite this