  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.
