Patent ID: 8463555

Claim:
A computer implemented method for nucleic acid sequence analysis, comprising: receiving sample nucleic acid sequence information comprising one or more mate pair sequences, wherein mate pair sequences comprise a first non-overlapping sequence and a second non-overlapping sequence separated by an intervening sequence; receiving a reference nucleic acid sequence information comprising at least one reference sequence; performing a first mapping operation for the sample nucleic acid sequence information using a processor to at least partially align the first non-overlapping sequence to the reference nucleic acid sequence, designating a window region comprising at least a portion of the at least one reference sequence based at least in part upon the alignment of the first non-overlapping sequence to the at least one reference sequence, performing a second mapping operation using a processor to at least partially align the second non-overlapping sequence to the designated window region of the reference sequence thereby positioning the first and second non-overlapping sequences with respect to one another, and outputting the results of the mapping operations.