Patent ID: 8571809

Claim:
A system for calculating scores of chains of sequence alignments of biological sequences, the system comprising: an integrated circuit that receives a query sequence and a database sequence, the integrated circuit comprising: a block that receives the query sequence; a block that receives from an index a plurality of subsequences of the database sequence; a block that identifies a plurality of alignment candidates of the query sequence; a block that identifies a first chain of alignments and a second chain of alignments between the plurality of alignment candidates and the plurality of subsequences; a block that scores the first chain of alignments and the second chain of alignments; and a block that performs dynamic programming in interalignment regions of the first chain of alignments and the second chain of alignments; an end extension process converting the plurality of alignment candidates into a plurality of extended alignment candidates; a joining process for joining the plurality of extended alignment candidates corresponding to the first chain of alignments and the second chain of alignments; outputting a first chain score of the first chain of alignments and a second chain score of the second chain of alignments, wherein each of the first chain of alignments and the second chain of alignments is a plurality of substantially exact character matches between characters of the plurality of alignment candidates of the query sequence and characters of the plurality of subsequences of the database sequence and a plurality of paths through a plurality of interalignment regions; and a computer that receives the first chain score and the second chain score and that displays the first chain score and the second chain score.