Difference between revisions of "Wikiomics:Orthologues"

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* [http://orthomcl.org/cgi-bin/OrthoMclWeb.cgi OrthoMCL] TribeMCL  
 
* [http://orthomcl.org/cgi-bin/OrthoMclWeb.cgi OrthoMCL] TribeMCL  
 
* [http://cd-hit.org/ CD-HIT] fast clustering of proteins and i.e. ESTs.
 
* [http://cd-hit.org/ CD-HIT] fast clustering of proteins and i.e. ESTs.
* [http://phylogenomics.berkeley.edu/cgi-bin/flowerpower/input_flowerpower.py FlowerPower]
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* [http://phylogenomics.berkeley.edu/cgi-bin/flowerpower/input_flowerpower.py FlowerPower] protein homology clustering algorithm, similar to PSI-BLAST in its iterated approach to alignment, profile construction, and homolog identification, but with distinct differences.  
FlowerPower is a protein homology clustering algorithm, similar to PSI-BLAST in its iterated approach to alignment, profile construction, and homolog identification, but with distinct differences.  
 
  
 
* [http://www.ebi.ac.uk/~guy/exonerate/exonerate.man.html Exonerate] tool from sanger
 
* [http://www.ebi.ac.uk/~guy/exonerate/exonerate.man.html Exonerate] tool from sanger

Revision as of 02:35, 17 July 2008

Protein orthologues

For simple orthologue retrieval in vertebrates use Ensembl. Each gene has there a list of best reciprocal hits in other species.

Review paper: PLOS One 2007

For clustering multiple sequences:

  • Inparanoid
  • OrthoMCL TribeMCL
  • CD-HIT fast clustering of proteins and i.e. ESTs.
  • FlowerPower protein homology clustering algorithm, similar to PSI-BLAST in its iterated approach to alignment, profile construction, and homolog identification, but with distinct differences.


Orthologues retrival