A method for comparing three genomes
BSB'05 Proceedings of the 2005 Brazilian conference on Advances in Bioinformatics and Computational Biology
kGC: finding groups of homologous genes across multiple genomes
BSB'11 Proceedings of the 6th Brazilian conference on Advances in bioinformatics and computational biology
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In this work, we propose n3GC, a method to infer a particular biological function in an organism, by finding homologous genes among three genomes, comparing the genes of the investigated organism with the genes of two other organisms, one having and the other not having this function. Our n3GC method takes as input previously identified families of paralogous genes in each one of the genomes, and produces a three set Venn diagram, each set representing a genome. The intersection of three (two) sets shows the families of similar genes having strong similarities among the three (two) genomes. The gene families of a genome not having strong similarities with any family of the other two genomes appear outside the intersections. We have used our method to determine potential pathogenic genes of the Paracoccidioides brasiliensis fungus, comparing it with seven fungi, three at a time, one pathogenic and the other non-pathogenic. To validate n3GC, we first investigate the Pfam classification of the families belonging to the intersections and compare with INPARANOID and 3GC methods.