Whole-genome protein sequences from Arabidopsis, Populus, Vitis, Glycine, Oryza, Brachypodium, Sorghum and Zea were merged and searched against themselves for homology using BLASTP with an E-value cutoff of 10−5. Default parameters of OrthoMCL (50 (link)) were used. The combination of OrthoMCL intermediate files ‘orthologs.txt’ and ‘coorthologs.txt’ (generated by orthomclDumpPairsFiles) was used as the whole set of ortholog pairs.
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Comparative Genomic Orthology Analysis
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Other organizations : University of Georgia, North China University of Science and Technology, J. Craig Venter Institute
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Variable analysis
independent variables
- Whole-genome protein sequences from Arabidopsis, Populus, Vitis, Glycine, Oryza, Brachypodium, Sorghum and Zea
- Homology between the merged protein sequences, as determined by BLASTP with an E-value cutoff of 10^-5
- Default parameters of OrthoMCL (50)
- The combination of OrthoMCL intermediate files 'orthologs.txt' and 'coorthologs.txt' (generated by orthomclDumpPairsFiles)
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