DNA Base-Calling from a Nanopore Using a Viterbi Algorithm

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DNA Base-Calling from a Nanopore Using a Viterbi Algorithm Winston Timp, Jeffrey Comer, Aleksei Aksimentiev Biophysical Journal Volume 102, Issue 10, Pages L37-L39 (May 2012) DOI: 10.1016/j.bpj.2012.04.009 Copyright © 2012 Biophysical Society Terms and Conditions

Figure 1 Viterbi algorithm as applied to nanopore base-calling. (A) Current values for all possible DNA triplets (43 = 64) simulated using atomic-resolution BD; error bars indicate the expected standard deviation in ionic current sampled at 1.6 μs. The green dashed line represents a typical current value for the GTG triplet (green point), and the red dashed line represents a typical current value for the TCG triplet (red point). Pictured in the inset is a simulated system for GCC. (B) The Viterbi algorithm operates on a state machine assumption. The operation of Viterbi's algorithm can be visualized by means of a trellis diagram; the Viterbi path is the path that maximizes the joint probabilities through the trellis, colored in orange. Biophysical Journal 2012 102, L37-L39DOI: (10.1016/j.bpj.2012.04.009) Copyright © 2012 Biophysical Society Terms and Conditions

Figure 2 Comparison of the Viterbi method and single current measurement for different SNR levels. Individual simulations base-calling λ DNA using either the Viterbi base-calling method (red) or single current values (black) are plotted as a bivariate histogram (binned hexagonally). Biophysical Journal 2012 102, L37-L39DOI: (10.1016/j.bpj.2012.04.009) Copyright © 2012 Biophysical Society Terms and Conditions