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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=Other=
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* [http://www.metazome.net/index.php Metazome] organizes the proteomes of twenty-four metazoans into gene families defined at nine ancestral nodes  on the metazoan evolutionary tree. Shows synthenty.
=References=
=References=

Revision as of 07:34, 7 December 2009

Contents

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

Other

  • Metazome organizes the proteomes of twenty-four metazoans into gene families defined at nine ancestral nodes on the metazoan evolutionary tree. Shows synthenty.

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.
  3. “PLoS ONE: Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes.” http://www.plosone.org/article/fetchArticle.action?articleURI=info:doi/10.1371/journal.pone.0000383.
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