Wikiomics:Orthologues

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==Orthologues retrival==
==Orthologues retrival==
* [http://orthomcl.cbil.upenn.edu/cgi-bin/OrthoMclWeb.cgi?rm=index OrthoMCL]
* [http://orthomcl.cbil.upenn.edu/cgi-bin/OrthoMclWeb.cgi?rm=index OrthoMCL]
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=References=
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1. “Joining forces in the quest for orthologs,” Text, 2009, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768974/.
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2. “Large-scale assignment of orthology: back to phylogenetics?,” Text, 2008, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760865/?tool=pubmed.

Revision as of 06:10, 7 December 2009

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

References

1. “Joining forces in the quest for orthologs,” Text, 2009, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768974/.

2. “Large-scale assignment of orthology: back to phylogenetics?,” Text, 2008, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760865/?tool=pubmed.

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