Viral phylogenomics using an alignment-free method: A three-step approach to determine optimal length of k-mer
Abstract
The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained >2 million viral genome sequences and a reference set of ~4000 viral genome sequences that cover a wide range of known viral families. Whole-genome sequences can be used to improve viral classification and provide insight into the viral tree of life . However, due to the lack of evolutionary conservation amongst diverse viruses, it is not feasible to build a viral tree of life using traditional phylogenetic methods based on conserved proteins. In this study, we used an alignment-free method that uses k-mers as genomic features for a large-scale comparison of complete viral genomes available in RefSeq. To determine the optimal feature length, k (an essential step in constructing a meaningful dendrogram), we designed a comprehensive strategy that combines three approaches: (1) cumulative relative entropy, (2) average number of common features among genomes, and (3) the Shannon diversity index. This strategy was used to determine k for all 3,905 complete viral genomes in RefSeq. Lastly, the resulting dendrogram shows consistency with the viral taxonomy of the ICTV and the Baltimore classificationmore »
- Authors:
-
- Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Arkansas for Medical Sciences, Little Rock, AR (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1351783
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Scientific Reports
- Additional Journal Information:
- Journal Volume: 7; Journal ID: ISSN 2045-2322
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 60 APPLIED LIFE SCIENCES; 96 KNOWLEDGE MANAGEMENT AND PRESERVATION; classification and taxonomy; genome informatics
Citation Formats
Zhang, Qian, Jun, Se -Ran, Leuze, Michael, Ussery, David, and Nookaew, Intawat. Viral phylogenomics using an alignment-free method: A three-step approach to determine optimal length of k-mer. United States: N. p., 2017.
Web. doi:10.1038/srep40712.
Zhang, Qian, Jun, Se -Ran, Leuze, Michael, Ussery, David, & Nookaew, Intawat. Viral phylogenomics using an alignment-free method: A three-step approach to determine optimal length of k-mer. United States. https://doi.org/10.1038/srep40712
Zhang, Qian, Jun, Se -Ran, Leuze, Michael, Ussery, David, and Nookaew, Intawat. Thu .
"Viral phylogenomics using an alignment-free method: A three-step approach to determine optimal length of k-mer". United States. https://doi.org/10.1038/srep40712. https://www.osti.gov/servlets/purl/1351783.
@article{osti_1351783,
title = {Viral phylogenomics using an alignment-free method: A three-step approach to determine optimal length of k-mer},
author = {Zhang, Qian and Jun, Se -Ran and Leuze, Michael and Ussery, David and Nookaew, Intawat},
abstractNote = {The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained >2 million viral genome sequences and a reference set of ~4000 viral genome sequences that cover a wide range of known viral families. Whole-genome sequences can be used to improve viral classification and provide insight into the viral tree of life . However, due to the lack of evolutionary conservation amongst diverse viruses, it is not feasible to build a viral tree of life using traditional phylogenetic methods based on conserved proteins. In this study, we used an alignment-free method that uses k-mers as genomic features for a large-scale comparison of complete viral genomes available in RefSeq. To determine the optimal feature length, k (an essential step in constructing a meaningful dendrogram), we designed a comprehensive strategy that combines three approaches: (1) cumulative relative entropy, (2) average number of common features among genomes, and (3) the Shannon diversity index. This strategy was used to determine k for all 3,905 complete viral genomes in RefSeq. Lastly, the resulting dendrogram shows consistency with the viral taxonomy of the ICTV and the Baltimore classification of viruses.},
doi = {10.1038/srep40712},
journal = {Scientific Reports},
number = ,
volume = 7,
place = {United States},
year = {Thu Jan 19 00:00:00 EST 2017},
month = {Thu Jan 19 00:00:00 EST 2017}
}
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