Patent ID: 6564151
Filing Date: 2003-05-13
Classification: G16B

Abstract:
A method for identifying pairs of proteins in a genome as being functionally linked, comprising:(a) providing a first plurality of protein sequences comprising substantially all protein sequences encoded by a first genome, or, a plurality of nucleic acid sequences comprising substantially all protein-encoding nucleic acid sequences in a first genotne; (b) providing a second plurality of protein sequences comprising substantially all protein sequences encoded by one or more additional genomes, or, a second plurality of nucleic acid sequences comprising substantially all protein-encoding nucleic acid sequences of one or more additional genomes; (c) comparing each protein sequence or nucleic acid sequence in the first plurality of protein sequences or nucleic acid sequences respectively with substantially all the protein sequences or nucleic acid sequences of the second plurality of protein sequences or nucleic acid sequences to determine if the protein sequence or nucleic acid sequence in the first genome has a homolog in the one or more additional genomes based on the degree of similarity of the sequences being compared; (d) generating a phylogenetic profile for each protein of the first genome, wherein the phylogenetic profile is a vector or pattern whose elements indicate whether a homolog of the protein or protein encoding nucleic acid sequence of the first genome is present or absent in each of the one or more additional genomes of the second plurality of protein sequences or nucleic acid sequences; and (e) linking proteins of the first genome having similar phylogenetic profiles, wherein proteins with similar profiles are identified as being functionally linked.