Biology subjects

Jene A Golovchenko

Publications and source records attributed to Jene A Golovchenko.

2 recordsLinked to original sources

bioRxiv2015

Thermal motion of DNA in an MspA pore

We report on an experiment and calculations that determine the thermal motion of a voltage-clamped ssDNA-NeutrAvidin complex in an MspA nanopore. The electric force and diffusion constant of DNA inside an MspA pore have been determined in order to evaluate DNAs thermal position fluctuations. We show that an out-of-equilibrium state returns to equilibrium so quickly that experiments usually measure a weighted average over the equilibrium position distribution. Averaging over the equilibrium position distribution is consistent with results of state-of-the-art nanopore sequencing experiments. It is shown that a reduction in thermal averaging can be achieved by increasing the electrophoretic force used in nanopore sequencing devices.

Biophysics↗

bioRxiv2015

A de novo DNA Sequencing and Variant Calling Algorithm for Nanopores

The single-molecule accuracy of nanopore sequencing has been an area of rapid academic and commercial advancement, but remains insufficient for the de novo analysis of genomes. We introduce here a novel algorithm for the error correction of nanopore data, utilizing statistical models of the physical system in order to obtain high accuracy de novo sequences at a range of coverage depths. We demonstrate the technique by sequencing M13 bacteriophage DNA to 99% accuracy at moderate coverage as well as its use in an assembly pipeline by sequencing {lambda} DNA at a range of coverages. We also show the algorithms ability to accurately classify sequence variants at far lower coverage than existing methods.

Bioinformatics↗