title: A fast and scalable kymograph alignment algorithm for nanochannel-based optical DNA mappings.
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.
authors: Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden; Division of Solid State Physics, Department of Physics, Lund University, Lund, Sweden.
authors: Charleston
authors: C
authors: Noble
authors: Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden.
authors: Adam N
authors: AN
authors: Nilsson
authors: Division of Solid State Physics, Department of Physics, Lund University, Lund, Sweden; Department of Physics, Gothenburg University, Gothenburg, Sweden.
authors: Camilla
authors: C
authors: Freitag
authors: Division of Solid State Physics, Department of Physics, Lund University, Lund, Sweden.
authors: Jason P
authors: JP
authors: Beech
authors: Division of Solid State Physics, Department of Physics, Lund University, Lund, Sweden.
authors: Jonas O
authors: JO
authors: Tegenfeldt
authors: Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden.
authors: Tobias
authors: T
authors: Ambjörnsson
mesh_terms: D000465:Algorithms; D001435:Bacteriophages / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods; D004247:DNA / Q000032:analysis*; D004279:DNA, Viral / Q000032:analysis; D023281:Genomics / Q000191:economics / Q000379:methods; D007734:Kymography / Q000191:economics / Q000379:methods*; D009038:Motion; D061848:Optical Imaging / Q000191:economics / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000191:economics / Q000379:methods*; D012984:Software; D013997:Time Factors
chemical_list: D004279:DNA, Viral; D004247:DNA