Patent ID: 7349811

Claim:
A method to design primers which identify and target a first nucleotide sequence derived from a first species wherein the expression of said first nucleotide sequence results in at least one phenotypic characteristic, the method comprising the steps of: providing a second nucleotide sequence that is known to encode a protein that results in the phenotypic characteristic; comparing the amino acid sequence encoded by the second nucleotide sequence to amino acid sequences cataloged in one or more databases that annotate amino acid sequences with phenotypic characteristics; extracting any cataloged amino acid sequences that contain a portion of the protein encoded by the second nucleotide sequence and which are annotated with said phenotypic characteristic; aligning the amino acid sequence encoded by the second nucleotide sequence to each extracted amino acid sequence; analyzing the extracted amino acid sequences based on at least percent similarity to find portions of said sequences having the highest percent similarity; reverse translating said portions of the aligned sequences to obtain nucleotide sequences that can be used to design primers that identify and target said first nucleotide sequence; designing one or more primers based on said reverse translated portions of the aligned sequences, which primers identify and target said first nucleotide sequence, and displaying the nucleotide sequence of said one or more primers.