A computational method system, and computer program are provided for inferri ng functional links from genome sequences. One method is based on the observati on that some pairs of proteins A' and B' have homologs in another organism fuse d into a single protein chain AB. A trans-genome comparison of sequences can reveal these AB sequences, which are Rosetta Stone sequences because they decipher an interaction between A' and B. Another method compares the genomi c sequence of two or more organisms to create a phylogenetic profile for each protein indicating its presence or absence across all the genomes. The profi le provides information regarding functional links between different families o f proteins. In yet another method a combination of the above two methods is us ed to predict functional links.
DETERMINING PROTEIN FUNCTION AND INTERACTION FROM GENOME ANALYSIS