Wikiomics:Orthologues

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* [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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=Other=
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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.
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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

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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