Dictionary coded profiles and their use with nanopore sequencers

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Lempel-Ziv complexity is the basis for widely used compression algorithms. It has also been proposed as the basis for a distance metric to measure evolutionary distance. In this work we present an extension of the latter idea to develop a low complexity robust species-specific genomic signature. This signature can be used to identify biological organisms using only a small fragment of their genome in a computationally efficient manner. We use this feature to develop an application to the increasingly popular, though error prone, nanopore single molecule sequencing. In this application we use the signature of the molecule being sequenced to rule out the presence of target organisms early in the sequencing process.

Original languageEnglish (US)
Title of host publication2017 IEEE International Conference on Electro Information Technology, EIT 2017
PublisherIEEE Computer Society
Pages422-426
Number of pages5
ISBN (Electronic)9781509047673
DOIs
StatePublished - Sep 27 2017
Event2017 IEEE International Conference on Electro Information Technology, EIT 2017 - Lincoln, United States
Duration: May 14 2017May 17 2017

Publication series

NameIEEE International Conference on Electro Information Technology
ISSN (Print)2154-0357
ISSN (Electronic)2154-0373

Other

Other2017 IEEE International Conference on Electro Information Technology, EIT 2017
CountryUnited States
CityLincoln
Period5/14/175/17/17

Fingerprint

Nanopores
Glossaries
Molecules
Genes

ASJC Scopus subject areas

  • Computer Science Applications
  • Information Systems
  • Control and Systems Engineering
  • Electrical and Electronic Engineering

Cite this

Murray, K., Dunigan, D. D., & Sayood, K. (2017). Dictionary coded profiles and their use with nanopore sequencers. In 2017 IEEE International Conference on Electro Information Technology, EIT 2017 (pp. 422-426). [8053398] (IEEE International Conference on Electro Information Technology). IEEE Computer Society. https://doi.org/10.1109/EIT.2017.8053398

Dictionary coded profiles and their use with nanopore sequencers. / Murray, Keith; Dunigan, David D.; Sayood, Khalid.

2017 IEEE International Conference on Electro Information Technology, EIT 2017. IEEE Computer Society, 2017. p. 422-426 8053398 (IEEE International Conference on Electro Information Technology).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Murray, K, Dunigan, DD & Sayood, K 2017, Dictionary coded profiles and their use with nanopore sequencers. in 2017 IEEE International Conference on Electro Information Technology, EIT 2017., 8053398, IEEE International Conference on Electro Information Technology, IEEE Computer Society, pp. 422-426, 2017 IEEE International Conference on Electro Information Technology, EIT 2017, Lincoln, United States, 5/14/17. https://doi.org/10.1109/EIT.2017.8053398
Murray K, Dunigan DD, Sayood K. Dictionary coded profiles and their use with nanopore sequencers. In 2017 IEEE International Conference on Electro Information Technology, EIT 2017. IEEE Computer Society. 2017. p. 422-426. 8053398. (IEEE International Conference on Electro Information Technology). https://doi.org/10.1109/EIT.2017.8053398
Murray, Keith ; Dunigan, David D. ; Sayood, Khalid. / Dictionary coded profiles and their use with nanopore sequencers. 2017 IEEE International Conference on Electro Information Technology, EIT 2017. IEEE Computer Society, 2017. pp. 422-426 (IEEE International Conference on Electro Information Technology).
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