Wikiomics:Orthologues: Difference between revisions
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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] | ||
=Other= | |||
* [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 05:34, 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.
- Exonerate tool from sanger
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
- “Joining forces in the quest for orthologs.” Text, 2009. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768974/.
- “Large-scale assignment of orthology: back to phylogenetics?.” Text, 2008. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760865/?tool=pubmed.
- “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.
