Sets of core genes were defined for nematodes, trematodes and cestodes for use as training sets for gene prediction.
Finding set of "core genes" for Nematoda, Trematoda and Cestoda
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posted 17 May, 2018
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"Core genes" are defined as genes shared by all species in a taxonomic group. Using the protocol, sets of core genes can be identified for such a group. These can then be used as training sets for gene prediction. This method describes the construction of sets of Nematode Orthologous Groups (NOGs)1, Trematode Orthologous Groups (TROGs) and Cestode Orthologous Groups (CEOGs).
compute cluster for parallel processing of multiple steps in OrthoMCL.
Building the NOGs and TROGs:
For the associated publication, the CEOGs were defined using a different set of cluster input since the OrthoMCL input for the steps above only include a single cestode:
Sets of HMM models for core genes of Nematoda, Trematoda and Cestoda which can be used for training gene prediction software.
Mitreva, M. et al. The draft genome of the parasitic nematode Trichinella spiralis. Nat Genet 43, 228-235, doi:10.1038/ng.769 (2011).
Li, L., Stoeckert, C. J., Jr. & Roos, D. S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13, 2178-2189, doi:10.1101/gr.1224503 (2003).