Issue 16, 2012

Fast and automatic processing of multi-level events in nanopore translocation experiments

Abstract

We have developed a method to analyze in detail, translocation events providing a novel and flexible tool for data analysis of nanopore experiments. Our program, called OpenNanopore, is based on the cumulative sums algorithm (CUSUM algorithm). This algorithm is an abrupt change detection algorithm that provides fitting of current blockages, allowing the user to easily identify the different levels in each event. Our method detects events using adaptive thresholds that adapt to low-frequency variations in the baseline. After event identification, our method uses the CUSUM algorithm to fit the levels inside every event and automatically extracts their time and amplitude information. This facilitates the statistical analysis of an event population with a given number of levels. The obtained information improves the interpretation of interactions between the molecule and nanopore. Since our program does not require any prior information about the analyzed molecules, novel molecule–nanopore interactions can be characterized. In addition our program is very fast and stable. With the progress in fabrication and control of the translocation speed, in the near future, our program could be useful in identification of the different bases of DNA.

Graphical abstract: Fast and automatic processing of multi-level events in nanopore translocation experiments

Supplementary files

Article information

Article type
Feature Article
Submitted
20 Apr 2012
Accepted
13 Jun 2012
First published
19 Jun 2012

Nanoscale, 2012,4, 4916-4924

Fast and automatic processing of multi-level events in nanopore translocation experiments

C. Raillon, P. Granjon, M. Graf, L. J. Steinbock and A. Radenovic, Nanoscale, 2012, 4, 4916 DOI: 10.1039/C2NR30951C

To request permission to reproduce material from this article, please go to the Copyright Clearance Center request page.

If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given.

If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page.

Read more about how to correctly acknowledge RSC content.

Social activity

Spotlight

Advertisements