Evaluation of Dynamic Time Warp Barycenter Averaging (DBA) for its Potential in Generating a Consensus Nanopore Signal for Genetic and Epigenetic Sequences
Date
2018-07
Journal Title
Journal ISSN
Volume Title
Publisher
IEEE
Abstract
Epigenetics is a chemical modification to DNA without changes in the base sequence. While it is known that epigenetic modifications have far reaching implications on how genes are expressed, it is difficult to identify what the modification is or where it can be found. A next-generation method of sequencing called nanopore sequencing may be the solution. Nanopore sequencing runs a voltage bias across the DNA sequence and outputs a unique electric response to each genetic unit. Epigenetic modifications may then be identified by their distinct electric response. In this paper we provide preliminary results of applying dynamic time warp Barycenter Averaging (DBA) to multiple noisy nanopore streams to generate a consensus signal that can be used to identify genetic sequences and their modifications. DBA convergence rates, time complexity, together with qualitative and quantitative metrics to compare the consensus signal with gold standards are evaluated.
Description
Keywords
dynamic time warp Barycenter Averaging, DBA, consensus signal, nanopore streams, genetic sequences and their modifications
Citation
Chan, S. L., Gordon, P. G., Smith, Michael R. (2018). Evaluation of Dynamic Time Warp Barycenter Averaging (DBA) for its Potential in Generating a Consensus Nanopore Signal for Genetic and Epigenetic Sequences, 40th International Conference of the IEEE Engineering in Medicine and Biology Society, Honolulu, Hawaii, July 17-21, 2018.