Dictionary coded profiles and their use with nanopore sequencers

Keith Murray; David D. Dunigan; Khalid Sayood

doi:10.1109/EIT.2017.8053398

Dictionary coded profiles and their use with nanopore sequencers

Keith Murray, David D. Dunigan, Khalid Sayood

Research output: Chapter in Book/Report/Conference proceeding › Conference 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 language	English (US)
Title of host publication	2017 IEEE International Conference on Electro Information Technology, EIT 2017
Publisher	IEEE Computer Society
Pages	422-426
Number of pages	5
ISBN (Electronic)	9781509047673
DOIs	https://doi.org/10.1109/EIT.2017.8053398
State	Published - Sep 27 2017
Event	2017 IEEE International Conference on Electro Information Technology, EIT 2017 - Lincoln, United States Duration: May 14 2017 → May 17 2017

Publication series

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

Other

Other	2017 IEEE International Conference on Electro Information Technology, EIT 2017
Country/Territory	United States
City	Lincoln
Period	5/14/17 → 5/17/17

ASJC Scopus subject areas

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

Access to Document

10.1109/EIT.2017.8053398

Cite this

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 proceeding › Conference 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

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Dictionary coded profiles and their use with nanopore sequencers

Abstract

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ASJC Scopus subject areas

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