Patent ID: 7386399

Claim:
A method for alignment of a plurality of data traces indicative of the positions of a plurality of nucleic acid base types in a target nucleic acid sequence, comprising the steps of: (a) selecting for each data trace one or more alignment points corresponding to an internal peak associated with internal bases that are highly conserved in the target nucleic acid, wherein said highly conserved internal bases are of expected type in at least 98 percent of actual samples, and further selecting alignment points selected from the group consisting of a primer peak associated with unextended primer, a full-length peak associated with full length product produced during a cyclic primer extension reaction with two primers, and assigning to each selected alignment point a reference position number reflecting the relative position of the alignment point with respect to the sequence as a whole; (b) assigning a sequence position number to each peak in each of the plurality of data traces that maximizes the number of times that the sequence position number and the reference position number are assigned to a base of the same type; (c) aligning the data traces based on the assigned sequence position numbers; (d) determining the sequence of the nucleic acid bases according to the aligned data traces; and (e) displaying the determined sequence of nucleic acid bases.