Introduction

We introduce a method (MONKEY) to identify conserved transcription-factor binding sites in multispecies alignments. MONKEY employs probabilistic models of factor specificity and binding-site evolution, on which basis we compute the likelihood that putative sites are conserved and assign statistical significance to each hit. Using genomes from the genus Saccharomyces, we illustrate how the significance of real sites increases with evolutionary distance and explore the relationship between conservation and function.

Publications

  1. MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model.
    Cite this
    Moses AM, Chiang DY, Pollard DA, Iyer VN, Eisen MB, 2004-01-01 - Genome biology

Credits

  1. Alan M Moses
    Developer

    Graduate Group in Biophysics, University of California, United States of America

  2. Derek Y Chiang
    Developer

  3. Daniel A Pollard
    Developer

  4. Venky N Iyer
    Developer

  5. Michael B Eisen
    Investigator

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT001446
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Submitted ByMichael B Eisen