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:
https://lup.lub.lu.se/record/5341783
- author
- Noble, Charleston
LU
; Nilsson, Adam
LU
; Freitag, Camilla
; Beech, Jason
LU
; Tegenfeldt, Jonas
LU
and Ambjörnsson, Tobias
LU
- organization
- publishing date
- 2015
- type
- Contribution to journal
- publication status
- published
- subject
- in
- PLoS ONE
- volume
- 10
- issue
- 4
- article number
- e0121905
- publisher
- Public Library of Science (PLoS)
- external identifiers
-
- pmid:25875920
- wos:000352845100052
- scopus:84929484482
- pmid:25875920
- 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
- 2016-04-01 13:58:41
- date last changed
- 2024-01-09 21:19:35
@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.}},
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 (PLoS)}},
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}},
doi = {{10.1371/journal.pone.0121905}},
volume = {{10}},
year = {{2015}},
}