Patent ID: 6892139

Claim:
A method for identifying a second nucleic acid sequence or second polypeptide sequence of a second protein, wherein the second protein has a biological or chemical property of interest, comprising: (a) providing a first nucleic acid sequence that encodes a first protein, or a first polypeptide sequence of the first protein, wherein the first protein has a biological or chemical property of interest; (b) providing an algorithm capable of analyzing a functional relationship between the first protein and second protein, wherein the algorithm is a “phylogenetic profile” method, wherein the “phylogenetic profile” method algorithm comprises (i) obtaining data comprising a plurality of sequences, wherein the plurality of sequences comprises a list of polypeptide sequences of proteins from at least two genomes or a list of nucleic acid sequences that encode proteins from at least two genomes; (ii) determining a protein phylogenetic profile for the first protein and for each protein of the plurality of sequences, wherein the protein phylogenetic profile indicates the presence or absence of a protein belonging to a particular protein family in each of the at least two genomes wherein the presence or absence of a protein in a particular protein family is determined by homology, wherein the homology between proteins is considered significant if a probability (p) of obtaining a higher homology score when the sequences are shuffled is below a probability (p) value threshold and wherein the probability (p) value threshold is set with respect to the value 1/NM, based on the total number of sequence comparisons that are to be performed, wherein N is the number of proteins in the first organism's genome and M is the number of proteins in all other genomes; (iii) grouping the proteins of the plurality of sequences based on similar profiles, wherein proteins with similar profiles are indicated to have a functional relationship; and (iv) comparing the first nucleic acid sequence or the first polypeptide sequence to the plurality of sequences by comparing the protein phylogenetic profile for the first protein to the protein phylogenetic profiles of the plurality of sequences to identify the second protein, whereby the second protein is selected from the members of the group with similar profiles as the first protein; and (c) comparing the first nucleic acid sequence or the first polypeptide sequence to a plurality of sequences using the algorithm as set forth in step (b) to identify the second nucleic acid sequence or second polypeptide sequence of the second protein which has a functional relationship to the first protein; thereby identifying a second nucleic acid sequence or a second polypeptide sequence of a second protein that possesses the property of interest.