Patent ID: 6047109
Filing Date: 2000-04-04
Classification: G16B

Abstract:
A method of maximizing open reading frame length in an assembly consensus sequence comprising:a. identifying frameshift ambiguities in the consensus sequence wherein the number of frameshift ambiguities is N;b. dividing the consensus sequence into N+1 fragments split by the identified frameshift ambiguities;c. generating a matrix of score values for each frameshift ambiguity in each frame from the fragment immediately following the frameshift ambiguity, where the matrix has N columns and three rows;d. applying a scoring metric that allocates a value to a translation product of a sequence from one or more fragments wherein the value reflects the likelihood that the sequence is a real coding sequence;e. repeating steps a through d for the reversed complement of the consensus sequence;f. rebuilding the consensus sequence wherein the highest scoring reading frame in the highest scoring direction is optimized; andg. displaying the results of step (f) on an output device.