Nanopore Detector Feedback Control Using Cheminformatics Methods Integrated with Labview/Labwindows Tools

Single biopolymers (DNA, RNA, or polypeptide) can be examined using an alpha-hemolysin channel detector. When a biopolymer is present in an alpha-hemolysin channel it can produce a highly structured ionic current blockade pattern, where the lifetimes at various sub-blockade levels reveal information about the kinetics of the biopolymer. Here we describe integration of LabVIEW/LabWindows automation capabilities with the "in-house" Channel Current Cheminformatics (CCC) software. Data acquired with LabVIEW/LabWindows is passed to the CCC software, on a streaming real time basis, for analysis and classification. The classification results are then quickly returned to the LabVIEW/LabWindows automation software for experimental feedback control. The prototype signal processing architecture is designed to rapidly extract useful information from noisy blockade signals. A fast, specially designed, generic Hidden Markov Model can be used for the channel current feature extraction. Classification of feature vectors obtained by the HMM can then be done by Support Vector Machines.

Name thesis:degree_name

M.S.

Level thesis:degree_level

Thesis

Discipline thesis:degree_discipline

Computer Science

Year

2006

Author dc:creator

• Sendamangalam, Srikanth

Contributors dc:contributor

• Winters-Hilt, Stephen
• Chen, Yixin
• Fu, Bin

Repository record dc:identifier

https://scholarworks.uno.edu/td/412

OAI identifier oai:identifier

oai:scholarworks.uno.edu:td-1433