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.
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* [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.  
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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.  
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* [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
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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.
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* [http://chibba.pgml.uga.edu/mcscan2/ MCScanX] is an algorithm to scan multiple genomes or subgenomes to identify putative homologous chromosomal regions, then align these regions using genes as anchors.
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=References=
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# “Joining forces in the quest for orthologs.” Text, 2009. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768974/.
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# “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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# “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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# "MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity." http://www.ncbi.nlm.nih.gov/pubmed/22217600
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[[Category:Protocol]]
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[[Category:In silico]]
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[[Category:Sequence analysis]]

Current revision

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.
  • MCScanX is an algorithm to scan multiple genomes or subgenomes to identify putative homologous chromosomal regions, then align these regions using genes as anchors.

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.
  4. "MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity." http://www.ncbi.nlm.nih.gov/pubmed/22217600
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