Evaluation of Dynamic Time Warp Barycenter Averaging (DBA) for its Potential in Generating a Consensus Nanopore Signal for Genetic and Epigenetic Sequences

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dc.contributor.authorChan, Rachel
dc.contributor.authorGordon, Paul M. K.
dc.contributor.authorSmith, Michael Richard
dc.date.accessioned2018-06-08T15:03:26Z
dc.date.available2018-06-08T15:03:26Z
dc.date.issued2018-07
dc.description.abstractEpigenetics 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.en_US
dc.description.grantingagencyNatural Sciences and Engineering Research Council - Discovery Granten_US
dc.identifier.citationChan, 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.en_US
dc.identifier.doihttp://dx.doi.org/10.11575/PRISM/31971
dc.identifier.urihttp://hdl.handle.net/1880/106742
dc.language.isoenen_US
dc.publisherIEEEen_US
dc.publisher.departmentElectrical and Computer Engineeringen_US
dc.publisher.facultySchulich School of Engineeringen_US
dc.publisher.hasversionPost-printen_US
dc.publisher.institutionUniversity of Calgaryen_US
dc.rightsUnless otherwise indicated, this material is protected by copyright and has been made available with authorization from the copyright owner. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission.en_US
dc.rights.urihttps://creativecommons.org/licenses/by/4.0en_US
dc.subjectdynamic time warp Barycenter Averagingen_US
dc.subjectDBAen_US
dc.subjectconsensus signalen_US
dc.subjectnanopore streamsen_US
dc.subjectgenetic sequences and their modificationsen_US
dc.titleEvaluation of Dynamic Time Warp Barycenter Averaging (DBA) for its Potential in Generating a Consensus Nanopore Signal for Genetic and Epigenetic Sequencesen_US
dc.typeconference paperen_US
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