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Face of Tobias Ambjörnsson. Photo.

Tobias Ambjörnsson

Senior lecturer

Face of Tobias Ambjörnsson. Photo.

A fast and scalable kymograph alignment algorithm for nanochannel-based optical DNA mappings.

Author

  • Charleston Noble
  • Adam Nilsson
  • Camilla Freitag
  • Jason Beech
  • Jonas Tegenfeldt
  • Tobias Ambjörnsson

Summary, in English

Optical mapping by direct visualization of individual DNA molecules, stretched in nanochannels with sequence-specific fluorescent labeling, represents a promising tool for disease diagnostics and genomics. An important challenge for this technique is thermal motion of the DNA as it undergoes imaging; this blurs fluorescent patterns along the DNA and results in information loss. Correcting for this effect (a process referred to as kymograph alignment) is a common preprocessing step in nanochannel-based optical mapping workflows, and we present here a highly efficient algorithm to accomplish this via pattern recognition. We compare our method with the one previous approach, and we find that our method is orders of magnitude faster while producing data of similar quality. We demonstrate proof of principle of our approach on experimental data consisting of melt mapped bacteriophage DNA.

Department/s

  • Computational Biology and Biological Physics
  • Solid State Physics
  • Atomic Physics
  • BioCARE: Biomarkers in Cancer Medicine improving Health Care, Education and Innovation
  • NanoLund

Publishing year

2015

Language

English

Publication/Series

PLoS ONE

Volume

10

Issue

4

Document type

Journal article

Publisher

Public Library of Science

Topic

  • Condensed Matter Physics
  • Biophysics

Status

Published

ISBN/ISSN/Other

  • ISSN: 1932-6203