Analysis of Nanopore Detector Measurements using Machine Learning Methods, with Application to Single-Molecule Kinetics

At its core, a nanopore detector has a nanometer-scale biological membrane across which a voltage is applied. The voltage draws a DNA molecule into an á-hemolysin channel in the membrane. Consequently, a distinctive channel current blockade signal is created as the molecule flexes and interacts with the channel. This flexing of the molecule is characterized by different blockade levels in the channel current signal. Previous experiments have shown that a nanopore detector is sufficiently sensitive such that nearly identical DNA molecules were classified successfully using machine learning techniques such as Hidden Markov Models and Support Vector Machines in a channel current based signal analysis platform [4-9]. In this paper, methods for improving feature extraction are presented to improve both classification and to provide biologists and chemists with a better understanding of the physical properties of a given molecule.

Name thesis:degree_name

M.S.

Level thesis:degree_level

Thesis

Discipline thesis:degree_discipline

Computer Science

Year

2007

Author dc:creator

• Landry, Matthew

Contributors dc:contributor

• Winters-Hilt, Stephen
• Nino, Jaime
• Richard, Golden

• Nanopore
• Hidden Markov Models
• Support Vector Machines
• Emission Variance Amplification
• Feature Extraction
• Channel Current Cheminformatics

Repository record dc:identifier

https://scholarworks.uno.edu/td/533

OAI identifier oai:identifier

oai:scholarworks.uno.edu:td-1533