UNIT 2.12 Using PhyloCon to Identify Conserved Regulatory Motifs

  1. Ting Wang

Published Online: 1 SEP 2007

DOI: 10.1002/0471250953.bi0212s19

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Wang, T. 2007. Using PhyloCon to Identify Conserved Regulatory Motifs. Current Protocols in Bioinformatics. 19:2.12:2.12.1–2.12.29.

Author Information

  1. University of California at Santa Cruz, Santa Cruz, California

Publication History

  1. Published Online: 1 SEP 2007
  2. Published Print: SEP 2007


Understanding gene regulation has been and remains one of the major challenges for the molecular biology community. Gene regulation is mediated by a variety of short DNA sequences called regulatory elements, which include transcription factor binding sites. A first step toward understanding gene regulation is the identification of regulatory elements present in the genome. This challenge has been defined as the “motif finding problem” in the field of computational biology. Over the past 20 years, many algorithms have been developed to tackle the motif finding problem computationally. The PhyloCon algorithm, developed in 2003, is one of the first motif finding algorithms that take advantage of two important data resources, i.e., phylogenetic conservation and gene co-regulation, to improve the efficiency of motif identification in biological datasets. This unit presents basic protocols to obtain, install, and apply the PhyloCon program and discusses the underlying algorithm and how to interpret the results. Curr. Protoc. Bioinform. 19:2.12.1-2.12.29. © 2007 by John Wiley & Sons, Inc.


  • motif discovery;
  • comparative genomics;
  • algorithm