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

Noble, Charleston LU ; Nilsson, Adam LU ; Freitag, Camilla; Beech, Jason LU ; Tegenfeldt, Jonas LU and Ambjörnsson, Tobias LU (2015) In PLoS ONE 10(4).
Abstract
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... (More)
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. (Less)
Please use this url to cite or link to this publication:
author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
PLoS ONE
volume
10
issue
4
publisher
Public Library of Science
external identifiers
  • pmid:25875920
  • wos:000352845100052
  • scopus:84929484482
ISSN
1932-6203
DOI
10.1371/journal.pone.0121905
language
English
LU publication?
yes
id
0049b0ec-50dd-4b0b-9655-3900f6b78258 (old id 5341783)
date added to LUP
2015-05-11 14:30:56
date last changed
2017-07-23 04:14:23
@article{0049b0ec-50dd-4b0b-9655-3900f6b78258,
  abstract     = {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.},
  articleno    = {e0121905},
  author       = {Noble, Charleston and Nilsson, Adam and Freitag, Camilla and Beech, Jason and Tegenfeldt, Jonas and Ambjörnsson, Tobias},
  issn         = {1932-6203},
  language     = {eng},
  number       = {4},
  publisher    = {Public Library of Science},
  series       = {PLoS ONE},
  title        = {A fast and scalable kymograph alignment algorithm for nanochannel-based optical DNA mappings.},
  url          = {http://dx.doi.org/10.1371/journal.pone.0121905},
  volume       = {10},
  year         = {2015},
}