TY - GEN
T1 - Dictionary coded profiles and their use with nanopore sequencers
AU - Murray, Keith
AU - Dunigan, David D.
AU - Sayood, Khalid
N1 - Publisher Copyright:
© 2017 IEEE.
PY - 2017/9/27
Y1 - 2017/9/27
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85033691246&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85033691246&partnerID=8YFLogxK
U2 - 10.1109/EIT.2017.8053398
DO - 10.1109/EIT.2017.8053398
M3 - Conference contribution
AN - SCOPUS:85033691246
T3 - IEEE International Conference on Electro Information Technology
SP - 422
EP - 426
BT - 2017 IEEE International Conference on Electro Information Technology, EIT 2017
PB - IEEE Computer Society
T2 - 2017 IEEE International Conference on Electro Information Technology, EIT 2017
Y2 - 14 May 2017 through 17 May 2017
ER -