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

Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

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.

Detaljer

Författare
Enheter & grupper
Externa organisationer
  • Lund University
  • Göteborgs universitet
Forskningsområden

Ämnesklassifikation (UKÄ) – OBLIGATORISK

  • Den kondenserade materiens fysik
  • Biofysik
Originalspråkengelska
Artikelnummere0121905
TidskriftPLoS ONE
Volym10
Utgivningsnummer4
StatusPublished - 2015
PublikationskategoriForskning
Peer review utfördJa