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A fast and scalable...
A fast and scalable kymograph alignment algorithm for nanochannel-based optical DNA mappings.
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- Noble, Charleston (författare)
- Lund University,Lunds universitet,Fasta tillståndets fysik,Fysiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Beräkningsbiologi och biologisk fysik - Genomgår omorganisation,Institutionen för astronomi och teoretisk fysik - Genomgår omorganisation,Naturvetenskapliga fakulteten,Solid State Physics,Department of Physics,Departments at LTH,Faculty of Engineering, LTH,Computational Biology and Biological Physics - Undergoing reorganization,Department of Astronomy and Theoretical Physics - Undergoing reorganization,Faculty of Science
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- Nilsson, Adam (författare)
- Lund University,Lunds universitet,Atomfysik,Fysiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Atomic Physics,Department of Physics,Departments at LTH,Faculty of Engineering, LTH
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- Freitag, Camilla (författare)
- Gothenburg University,Göteborgs universitet,University of Gothenburg,Lund University,Institutionen för fysik (GU),Department of Physics (GU)
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- Beech, Jason (författare)
- Lund University,Lunds universitet,Fasta tillståndets fysik,Fysiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Solid State Physics,Department of Physics,Departments at LTH,Faculty of Engineering, LTH
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- Tegenfeldt, Jonas (författare)
- Lund University,Lunds universitet,Fasta tillståndets fysik,Fysiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Solid State Physics,Department of Physics,Departments at LTH,Faculty of Engineering, LTH
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- Ambjörnsson, Tobias (författare)
- Lund University,Lunds universitet,Beräkningsbiologi och biologisk fysik - Genomgår omorganisation,Institutionen för astronomi och teoretisk fysik - Genomgår omorganisation,Naturvetenskapliga fakulteten,Computational Biology and Biological Physics - Undergoing reorganization,Department of Astronomy and Theoretical Physics - Undergoing reorganization,Faculty of Science
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(creator_code:org_t)
- 2015-04-13
- 2015
- Engelska.
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:4
- Relaterad länk:
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http://dx.doi.org/10... (free)
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https://journals.plo...
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https://lup.lub.lu.s...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- 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.
Ämnesord
- NATURVETENSKAP -- Fysik -- Den kondenserade materiens fysik (hsv//swe)
- NATURAL SCIENCES -- Physical Sciences -- Condensed Matter Physics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Biofysik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biophysics (hsv//eng)
- NATURVETENSKAP -- Fysik -- Annan fysik (hsv//swe)
- NATURAL SCIENCES -- Physical Sciences -- Other Physics Topics (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences (hsv//eng)
- NATURVETENSKAP -- Fysik (hsv//swe)
- NATURAL SCIENCES -- Physical Sciences (hsv//eng)
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- art (ämneskategori)
- ref (ämneskategori)
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