Patent ID: 7561974

Claim:
A system for identifying genes, comprising: a pattern database comprising patterns of amino acids; an input device for inputting a genomic DNA sequence; and a processor which is configured to: translate an open reading frame (ORF) of said DNA sequence into an amino acid translation; assign weights, w i , to said patterns of amino acids, said weights being given by the equation w i =log p i −log q i , where p i is a probability that a pattern matches an actual amino acid sequence at a fixed location, and q i is a probability that said pattern matches an amino acid translation of a non-coding ORF; locate in said amino acid translation occurrences of said weighted patterns, and assign a coding quality measure for said ORF which is given by Ws = ∑ i = 1 m ⁢ ⁢ w i , where m is the number of patterns which are located in said amino acid translation of said ORF; and identify said open reading frame as including a putative gene if a value of said coding quality measure is greater than a predetermined threshold value.