bio-MOSAIC 1.0 – Multiple Orthologous Sequence Analysis and Integration by Cluster optimization

bio-MOSAIC 1.0

:: DESCRIPTION

bio-MOSAIC (MOSAIC) is the first tool for integrating methodologically diverse OD (Ortholog detection) methods.  IT is designed to provide a great deal of flexibility in the construction and optimization of orthogolous clusters.

::DEVELOPER

The Hernandez Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

   bio-MOSAIC

:: MORE INFORMATION

Citation

G3 (Bethesda). 2015 Feb 23;5(4):629-38. doi: 10.1534/g3.115.017095.
Rock, paper, scissors: harnessing complementarity in ortholog detection methods improves comparative genomic inference.
Maher MC, Hernandez RD

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

TreeGibbsSampler

:: 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.

PhyME – Find Motifs in sets of Orthologous Sequences

PhyME

:: DESCRIPTION

PhyME (Phylogenetic Motif Elicitation) is a software tool for finding motifs in sets of orthologous sequences.PhyME is an ab initio motif-finding algorithm, which finds overrepresented motifs in input sequences while accounting for their evolutionary conservation in orthologs of those sequences.

PhyME discovers motifs by integrating two important aspects of the motif’s significance, overrepresentation and interspecies conservation, into one probabilistic score. The algorithm is based on multiple alignment and expectation-maximization.

::DEVELOPER

The Sinha Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

PhyME

:: MORE INFORMATION

  • S. Sinha, “PhyME: a software tool for finding motifs in sets of orthologous sequences”, Methods Mol. Biol., vol. 395 (2007) 309-18. Pubmed 17993682.
  • S. Sinha, M. Blanchette, M. Tompa, “PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences”, BMC Bioinformatics, vol. 5(2004) 170. Pubmed 15511292.