Tree Gibbs Sampler: identifying conserved motifs without aligning orthologous sequences

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...

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Bibliographic Details
Published in:Bioinformatics 2007-08, Vol.23 (15), p.2013-2014
Main Authors: Cai, Xiaohui, Hu, Haiyan, Li, Xiaoman Shawn
Format: Article
Language:English
Subjects:
Algorithms
Amino Acid Motifs - genetics
Biological and medical sciences
Conserved Sequence - genetics
Evolution, Molecular
Fundamental and applied biological sciences. Psychology
General aspects
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Proteins - genetics
Sequence Alignment - methods
Sequence Analysis, DNA - methods
Sequence Homology, Nucleic Acid
Software
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Description
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 Contact: shawnli@iupui.edu
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btm282