Method and apparatus for alignment of signals for use in DNA base-calling

An apparatus for determining the sequence of a nucleic acid polymer comprising:

• (a) an electrophoresis gel holder;
• (b) first and second electrodes disposed to apply an electric field to the electrophoresis gel disposed within the electrophoresis gel holder to cause oligonucleotide fragments loaded on the electrophoresis gel to migrate within the electrophoresis gel;
• (c) a detection system comprising an interrogating beam and a detector for detecting the passage of oligonucleotide fragments through a detection zone;
• and
• (d) a data processing system operatively connected to the detector for receiving four data traces, one for each of four chain termination product mixtures for the nucleic acid polymer, wherein the data processing system has stored therein a programmed instruction set effective to
• identify peaks in each of the four data traces;
• combine the four data traces in an initial alignment;
• determine coefficients of shift and stretch for selected data points within each data trace, said coefficients optimizing a cost function which reflects the suitability of a trial alignment resulting from the application of the trial stretch and shift coefficients to the combined data traces;
• generate a warp function for each data trace from the coefficients of shift and stretch determined for the selected data points;
• apply each warp functions to the respective data trace to produce four warped data traces;
• and
• assemble the four warped data traces to form an aligned data set.