Patent ID: 6772069
Filing Date: 2004-08-03
Classification: G16B

Abstract:
A method for identifying a high confidence functional link between at least two proteins, comprising the following steps:(a) identifying non-homologous proteins as being functionally linked by a â€œRosetta Stoneâ€  method conprising the following steps (i) providing amino acid sequences of a first protein and a second protein, wherein the first and second proteins are not homologous, (ii) providing an amino acid sequence of a third protein, (iii) aligning atnino acid sequence segments from the first protein and the second protein to the amino acid sequence of the third protein, wherein the amino acid sequence segments from the first and the second protein do not align to each other with any significant sequence similarity, and (iv) establishing whether the first and second proteins are functionally linked by determining whether a significant sequence similarity is present between the aligned amino acid sequences of step (iii), thereby identifying non-homologous proteins as being functionally linked; (b) identifying pairs of proteins in a genome as being functionally linked by a â€œphylogenetic profileâ€  method comprising the following steps (i) providing a first plurality of protein sequences comprising substantially all protein sequences encoded by a first genome, (ii) providing a second plurality of protein sequences comprising substantially all protein sequences encoded by one or more additional genomes, (iii) comparing each protein sequence in the first plurality of protein sequences with substantially all the protein sequences of the second plurality of protein sequences to determine if a protein 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, (iv) 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 corresponding protein is present or absent in the one or more additional genomes, and (v) grouping together proteins having similar phylogenetic profiles, wherein a similar phylogenetic profile indicates a functional link between the proteins; and (c) identifying pairs of proteins that are linked in both (a) and (b), thereby identifying a high confidence functional link between at least two proteins.