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The COG database: an updated version includes eukaryotes
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The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies. We describe here a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins COGs from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eu k aryotic o rthologous g roups.
The eu k aryotic o rthologous g roups KOGs include proteins from 7 eukaryotic genomes: three animals the nematode Caenorhabditis elegans , the fruit fly Drosophila melanogaster and Homo sapiens , one plant, Arabidopsis thaliana , two fungi Saccharomyces cerevisiae and Schizosaccharomyces pombe , and the intracellular microsporidian parasite Encephalitozoon cuniculi. Compared to the coverage of the prokaryotic genomes with COGs, a considerably smaller fraction of eukaryotic genes could be included into the KOGs; addition of new eukaryotic genomes is expected to result in substantial increase in the coverage of eukaryotic genomes with KOGs.
In part, this difference is probably due to the small number of included eukaryotic genomes, but it could also reflect the relative compactness of eukaryotes as a clade and the greater evolutionary stability of eukaryotic genomes. The updated collection of orthologous protein sets for prokaryotes and eukaryotes is expected to be a useful platform for functional annotation of newly sequenced genomes, including those of complex eukaryotes, and genome-wide evolutionary studies.
The rapid accumulation of genome sequences is a major challenge to researchers attempting to extract the maximum functional and evolutionary information from the new genomes.
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Bruner, Natalie R., “Discriminative-stimulus and time-course effects of kava-kava (Piper methysticum) in rats” (). To date, there is no research examining whether kava shares discriminative-stimulus constant levels and there was a reversed hour light-dark cycle in effect. Advisor: James D. Dougan,. Ph.D.
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