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.
Publication types
-
Research Support, Non-U.S. Gov't
MeSH terms
-
Algorithms*
-
Bacteriophages / genetics
-
Chromosome Mapping / methods
-
DNA / analysis*
-
DNA, Viral / analysis
-
Genomics / economics
-
Genomics / methods
-
Kymography / economics
-
Kymography / methods*
-
Motion
-
Optical Imaging / economics
-
Optical Imaging / methods*
-
Sequence Analysis, DNA / economics
-
Sequence Analysis, DNA / methods*
-
Software
-
Time Factors
Associated data
-
figshare/10.6084/M9.FIGSHARE.1312910
Grants and funding
TA, Swedish Research Council, grant no. 2009-2924,
http://www.vr.se/ Funding provided to JOT, 2007-584, Swedish Research Council, grant no. 2007-584,
http://www.vr.se/, JOT, VINNOVA, grant number P35735-1,
http://www.vinnova.se/en/, TA, The Carl Tryggers Foundation grant no. 12:13
http://www.carltryggersstiftelse.se/, and JOT, The Hasselblad Foundation
http://www.hasselbladfoundation.org/news. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.