Wikiomics:Orthologues: Difference between revisions
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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] | * [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. | ||
* [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 03:35, 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.
- Exonerate tool from sanger
