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Using the Gibbs Motif Sampler for phylogenetic footprinting
William Thompson1, Sean Conlan, Lee Ann McCue
1Center for Computational Molecular Biology, Brown Unversity.
Methods in Molecular Biology (Clifton, N.J.)
|November 13, 2007
Summary
The Gibbs Motif Sampler software aids in identifying transcription factor binding sites (TFBSs). This study demonstrates its use in phylogenetic footprinting to find conserved TFBSs in bacterial promoter sequences.
Area of Science:
- Bioinformatics
- Genomics
- Molecular Biology
Background:
- The Gibbs Motif Sampler (Gibbs) is a computational tool for identifying conserved patterns in biological sequences.
- Its primary application involves predicting transcription factor binding sites (TFBSs) within gene promoter regions.
Purpose of the Study:
- To describe methods utilizing Gibbs for TFBS prediction in orthologous nucleotide sequences, a technique known as phylogenetic footprinting.
- To illustrate the application of Gibbs for detecting specific TFBSs, exemplified by the transcription factor LexA.
Main Methods:
- Employing the Gibbs Motif Sampler software for sequence analysis.
- Applying phylogenetic footprinting by analyzing collections of orthologous nucleotide sequences.
- Utilizing representative species from two proteobacterial divisions for data analysis.
Main Results:
- Demonstrated the efficacy of Gibbs in locating conserved motifs, specifically TFBSs, within promoter regions.
- Successfully identified binding sites for the transcription factor LexA in orthologous sequences.
Conclusions:
- Phylogenetic footprinting using Gibbs is a viable approach for discovering TFBSs in related species.
- The Gibbs Motif Sampler is effective for identifying functional elements like TFBSs across different bacterial lineages.
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