Tree Gibbs Sampler: identifying conserved motifs without aligning orthologous sequences

Xiaohui Cai; Haiyan Hu; Xiaoman Shawn Li

doi:10.1093/bioinformatics/btm282

Tree Gibbs Sampler: identifying conserved motifs without aligning orthologous sequences

Bioinformatics. 2007 Aug 1;23(15):2013-4. doi: 10.1093/bioinformatics/btm282. Epub 2007 May 31.

Authors

Xiaohui Cai¹, Haiyan Hu, Xiaoman Shawn Li

Affiliation

¹ Division of Biostatistics, School of Medicine, Indiana University, Indianapolis, IN 46202, USA.

PMID: 17540681
DOI: 10.1093/bioinformatics/btm282

Abstract

Summary: Tree Gibbs Sampler is a software for identifying motifs by simultaneously using the motif overrepresentation property and the motif evolutionary conservation property. It identifies motifs without depending on pre-aligned orthologous sequences, which makes it useful for the extraction of regulatory elements in multiple genomes of both closely related and distant species.

Availability: The Tree Gibbs Sampler software is freely downloadable at https://compbio.iupui.edu/xiaomanli/LiSoftware/retrieve.php?ID=tgs

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Amino Acid Motifs / genetics*
Conserved Sequence / genetics*
Evolution, Molecular*
Proteins / genetics*
Sequence Alignment / methods
Sequence Analysis, DNA / methods*
Sequence Homology, Nucleic Acid
Software*

Substances

Proteins