What are the differences among different ortholog group databases?
The ortholog group databases differ mainly in three ways: the species included in the ortholog group construction, the type of data, and the method of ortholog group construction. In general, the wider the species distribution is, the more ancient the ortholog groups tend to be. Sometimes it means that paralogs that arose more recently in closely-related species will be grouped into one ortholog group. So you should base your choice of ortholog database on your preference for how specific you would like the ortholog groups to be. Currently, the NCBI COG database contains 66 genomes that include mostly prokaryotes and three eukaryotes. NCBI KOG database contains 7 fully sequenced eukaryotic genomes. OrthoMCL DB includes 55 genomes with more evenly distributed prokaryotic and eukaryotic species. MultiParanoid contains 4 animals: human, fly, worm and sea squirt. TIGR EGO is built on the sequences from 82 eukaryotic species. With the exception of TIGR EGO, which uses DNA sequences in ortho
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