Patent ID: 8165821

Claim:
A computer implemented method of nucleic acid sequence analysis, comprising: receiving first nucleic acid sequence information comprising one or more mate pair sequences, wherein mate pair sequences comprise a first non-overlapping pairwise sequence and a second non-overlapping pairwise sequence separated by an intervening sequence length; receiving second nucleic acid sequence information comprising at least one reference sequence; performing a computer assisted mapping operation for the mate pair sequences in which the first non-overlapping pairwise sequence and the second non-overlapping pairwise sequence for a respective mate pair are aligned to the at least one reference sequence using a processor by the steps of: performing a first mapping operation using a processor to align the first non-overlapping pairwise sequence of the mate pair sequences to the at least one reference sequence with a first selected mismatch constraint, identifying mate pair sequences having first non-overlapping pairwise sequences which are aligned to the at least one reference sequence while satisfying the selected mismatch constraint, designating a window region within the at least one reference sequence for the identified mate pair sequences based on the alignment of the first non-overlapping pairwise sequence to the at least one reference sequence, performing a second mapping operation using a processor to align the second non-overlapping pairwise sequence to the window region of the reference sequence with a second selected mismatch constraint, identifying mate pair sequences with first and second non-overlapping pairwise sequences that have mapped to the at least one reference sequence following performing the first and second mapping operations; and, outputting the results of the mapping operations.