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Figure 3 | BMC Bioinformatics

Figure 3

From: Nanopore-based kinetics analysis of individual antibody-channel and antibody-antigen interactions

Figure 3

Antibody toggle signal and HMM signal profile. On the left is capture event of an antibody molecule which has yielded a toggle signal. The first portion of the signal is at the 120 pA current reading, standard for an open alpha-hemolysin channel. A sudden drop of the ionic current indicates a physical blockade of the channel has occurred reducing its current flow. On the right: An HMM is used to remove noise from the acquired signals, and to extract features from them. The HMM is implemented with fifty states. Each blockade signature is de-noised by 5 rounds of Expectation-Maximization (EM) training on the parameters of the HMM. After the EM iterations, 150 parameters are extracted from the HMM. The 150 feature vectors obtained from the 50-state HMM-EM/Viterbi implementation are: the 50 dwell percentages in the different blockade levels from the Viterbi trace-back states, the 50 variances of the emission probability distributions associated with the different states, and the 50 merged transition probabilities from the primary and secondary blockade occupation levels (meant to work well with two-state dominant modulatory blockade signals).

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