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

Summary, in English

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: Charleston Noble; Adam Nilsson; Camilla Freitag; Jason Beech; Jonas Tegenfeldt; Tobias Ambjörnsson
• Department/s: Computational Biology and Biological Physics - Has been reorganised; Solid State Physics; Atomic Physics; BioCARE: Biomarkers in Cancer Medicine improving Health Care, Education and Innovation; NanoLund: Centre for Nanoscience
• Publishing year: 2015
• Language: English
• Publication/Series: PLoS ONE
• Volume: 10
• Issue: 4
• Links: http://dx.doi.org/10.1371/journal.pone.0121905
• Document type: Journal article
• Publisher: Public Library of Science (PLoS)
• Topic: Condensed Matter Physics; Biophysics; Other Physics Topics
• Status: Published
• ISBN/ISSN/Other: ISSN: 1932-6203