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Using the Gibbs Motif Sampler for Phylogenetic Footprinting

  • William Thompson
  • Sean Conlan
  • Lee Ann McCue
  • Charles E. Lawrence
Part of the Methods in Molecular Biology™ book series (MIMB, volume 395)

Summary

The Gibbs Motif Sampler (Gibbs) is a software package used to predict conserved elements in biopolymer sequences. Although the software can be used to locate conserved motifs in protein sequences, its most common use is the prediction of transcription factor binding sites (TFBSs) in promoters upstream of gene sequences. We will describe approaches that use Gibbs to locate TFBSs in a collection of orthologous nucleotide sequences, i.e., phylogenetic footprinting. To illustrate this technique, we present examples that use Gibbs to detect binding sites for the transcription factor LexA in orthologous sequence data from representative species belonging to two different proteobacterial divisions.

Key Words

Gibbs sampling phylogenetic footprinting transcription regulation 

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Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  • William Thompson
    • 1
  • Sean Conlan
    • 2
  • Lee Ann McCue
    • 3
  • Charles E. Lawrence
    • 4
  1. 1.Center for Computational Molecular BiologyBrown UniversityUSA
  2. 2.New York Department of HealthThe Wadsworth CenterUSA
  3. 3.Computational Biology and Bioinformatics, Pacific Northwest National LaboratoryUSA
  4. 4.Center for Computational Molecular BiologyBrown UniversityUSA

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