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Using HMMs to Quantify Signals from DNA Driven Through a Nanometer Scale Pore



Vincent M. Stanford, John J. Kasianowicz


It was recently shown that individual molecules of single-stranded DNA can be forced through a nanoscale pore by an electric field. We demonstrate signal processing methods to detect and measure sub-states in the DNA-induced current blockades during transport. The current flow is approximately piecewise stationary during these transport events, and we used an ergodic HMM to make maximum likelihood estimates of the event sub-states. Interestingly, the signal amplitude distributions caused by polynucleotides with the same length and composition depends on the direction the polymers transit the pore. Our methods indicate automatic extraction of structural information from individual DNA molecules is possible.
Proceedings Title
2002 Genomic Signal Processing Conference,
Conference Dates
October 11-13, 2002
Conference Title
IEEE Workshop on Genomic Signal Processing and Statistics


alpha-hemolysin, hidden Markov model, HMM, ion channel, maximum likelihood estimation, MLE


Stanford, V. and Kasianowicz, J. (2002), Using HMMs to Quantify Signals from DNA Driven Through a Nanometer Scale Pore, 2002 Genomic Signal Processing Conference, (Accessed June 12, 2024)


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Created October 1, 2002, Updated February 17, 2017