Patent Document ID: 8280640
Application ID: 10916370
Patent Flag: 1

Claim One:
1. A method of comparing sequential data using a computer system, comprising: (a) providing to a first storage device a target sequence having at least a first binary string n bits in length and a second binary string n bits in length, the second binary string aligned with the first binary string to form n groups of aligned bits, each group of aligned bits including one bit from the first string and the corresponding bit from the second string, each group of aligned bits defining a component member of the target sequence; (b) providing to a second storage device a query sequence having at least a first binary string m bits in length (m≦n) and a second binary string m bits in length, the second binary string aligned with the first binary string to form m groups of aligned bits, each group of aligned bits including one bit from the first string and the corresponding bit from the second string, each group of aligned bits defining a component member of the query sequence; (c) comparing the m bits contained in the first binary string of the query sequence against the n bits contained in the first binary string of the target sequence to determine first matches between the first binary string of the query sequence and the first binary string of the target sequence, each first match, if any, defining an m-bit segment having a match position m bits in length in the first binary string of the target sequence, and, for each first match, if any, associating the match position in the first binary string of the target sequence to the corresponding m-bit segment of the second binary string of the target sequence; (d) for each first match, if any, comparing the m bits contained in the second binary string of the query sequence against m-bit segments of the second binary string of the target sequence corresponding to such first match to determine second matches, if any, between the target and query sequences; (e) generating an indication of matches, if any, between one or more of the binary strings of the target sequence and the binary strings of the query sequence and outputting said indication to a user interface.