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MOSAIC: A Modular Single-Molecule Analysis Interface for Decoding Multistate Nanopore Data

Forstater, Jacob H., Briggs, Kyle, Robertson, Joseph W. F., Ettedgui, Jessica, Marie-Rose, Olivier, Vaz, Canute, Kasianowicz, John J., Tabard-Cossa, Vincent, Balijepalli, Arvind
Analytical chemistry 2016 v.88 no.23 pp. 11900-11907
algorithms, analytical methods, computer software, medicine, models, nanopores, single-stranded DNA
Biological and solid-state nanometer-scale pores are the basis for numerous emerging analytical technologies for use in precision medicine. We developed Modular Single-Molecule Analysis Interface (MOSAIC), an open source analysis software that improves the accuracy and throughput of nanopore-based measurements. Two key algorithms are implemented: ADEPT, which uses a physical model of the nanopore system to characterize short-lived events that do not reach their steady-state current, and CUSUM+, a version of the cumulative sum statistical method optimized for longer events that do. We show that ADEPT detects previously unreported conductance states that occur as double-stranded DNA translocates through a 2.4 nm solid-state nanopore and reveals new interactions between short single-stranded DNA and the vestibule of a biological pore. These findings demonstrate the utility of MOSAIC and the ADEPT algorithm, and offer a new tool that can improve the analysis of nanopore-based measurements.