Patent ID: 8182993

Claim:
A method of identifying a nucleotide in a nucleic acid sequence, comprising: receiving a first optical signal from a reaction that produces optical signals during a template dependent primer extension reaction, wherein the first optical signal is emitted from a detectable label on a polyphosphate chain of a nucleotide analog, the detectable label is liberated from the nucleotide analog during an incorporation of the nucleotide analog in the template dependent primer extension reaction, and an optical pulse width of the first optical signal correlates with an amount of time the nucleotide analog is associated with a polymerase prior to liberation of the detectable label; classifying the first optical signal as a significant pulse based upon at least one of the optical pulse width of the first optical signal and an intensity of the first optical signal; associating the first optical signal with a spectrally distinguishable signal profile that correlates to a particular dye spectrum; when the first optical signal is (i) deemed a significant pulse by the classifying and (ii) is associated with a spectrally distinguishable signal profile by the associating, determining whether the first optical signal is an incorporation event based upon a signal environment around the first optical signal, wherein the signal environment includes a characterization of an optical signal preceding the first optical signal or a characterization of an optical signal that comes after the first optical signal; and identifying the nucleotide in the nucleic acid sequence when the first optical signal is determined to be an incorporation event, wherein the receiving, classifying, associating, determining, or identifying is performed using a suitably programmed computer.