Unit

UNIT 2.8 Using the Gibbs Motif Sampler to Find Conserved Domains in DNA and Protein Sequences

  1. William Thompson1,
  2. Lee Ann McCue2,
  3. Charles E. Lawrence1

Published Online: 1 JUL 2005

DOI: 10.1002/0471250953.bi0208s10

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Thompson, W., McCue, L. A. and Lawrence, C. E. 2005. Using the Gibbs Motif Sampler to Find Conserved Domains in DNA and Protein Sequences. Current Protocols in Bioinformatics. 10:2.8:2.8.1–2.8.42.

Author Information

  1. 1

    Brown University, Providence, Rhode Island

  2. 2

    Center for Bioinformatics The Wadsworth Center New York State Department of Health, Albany, New York

Publication History

  1. Published Online: 1 JUL 2005
  2. Published Print: JUN 2005

Abstract

The Gibbs Motif Sampler (Gibbs) is a software package for discovering conserved elements in biopolymer sequences. This unit describes the basic operation of the Web-based interface to Gibbs, along with advanced examples of its use, and the Web interface to dscan, a sequence database search program.

Keywords:

  • Gibbs sampling;
  • Transcription factor binding site;
  • Sequence Alignment;
  • Motif;
  • DNA;
  • Protein;
  • Phylogentic Footprinting;
  • Stochastic Algorithm;
  • Markov Chain Monte-Carlo;
  • Bayesian statistics