Entropic Profiler – Extract and Study Conserved Motifs in Genomes

Entropic Profiler

:: DESCRIPTION

The Entropic Profiler application here presented is a new tool designed to detect and extract under and over-represented DNA segments in genomes by using EP. It allows its computation in a very efficient way by recurring to improved algorithms and data structures, which include modified suffix trees.

::DEVELOPER

Systems Biomedicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C Compiler

:: DOWNLOAD

Entropic Profiler

:: MORE INFORMATION

Citation

BMC Res Notes. 2009 May 5;2:72. doi: 10.1186/1756-0500-2-72.
Entropic Profiler – detection of conservation in genomes using information theory.
Fernandes F, Freitas AT, Almeida JS, Vinga S.

TreeGibbsSampler – Identifying Conserved Motifs without Aligning Orthologous Sequences

TreeGibbsSampler

:: DESCRIPTION

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.

::DEVELOPER

Xiaohui Cai, Haiyan Nancy Hu ,Xiaoman Shawn Li

:: SCREENSHOTS

:: REQUIREMENTS

Linux/ Windows

:: DOWNLOAD

Tree Gibbs Sampler

:: MORE INFORMATION

Citation:

Bioinformatics. 2007 Aug 1;23(15):2013-4. Epub 2007 May 31.
Tree Gibbs Sampler: identifying conserved motifs without aligning orthologous sequences.
Cai X, Hu H, Li XS.