ClassyFlu: Classification of Influenza A Viruses with Discriminatively Trained Profile-HMMs
Abstract
Accurate and rapid characterization of influenza A virus (IAV) hemagglutinin (HA) and neuraminidase (NA) sequences with respect to subtype and clade is at the basis of extended diagnostic services and implicit to molecular epidemiologic studies. ClassyFlu is a new tool and web service for the classification of IAV sequences of the HA and NA gene into subtypes and phylogenetic clades using discriminatively trained profile hidden Markov models (HMMs), one for each subtype or clade. ClassyFlu merely requires as input unaligned, full-length or partial HA or NA DNA sequences. It enables rapid and highly accurate assignment of HA sequences to subtypes H1–H17 but particularly focusses on the finer grained assignment of sequences of highly pathogenic avian influenza viruses of subtype H5N1 according to the cladistics proposed by the H5N1 Evolution Working Group. NA sequences are classified into subtypes N1–N10. ClassyFlu was compared to semiautomatic classification approaches using BLAST and phylogenetics and additionally for H5 sequences to the new ‘‘Highly Pathogenic H5N1 Clade Classification Tool’’ (IRD-CT) proposed by the Influenza Research Database. Our results show that both web tools (ClassyFlu and IRD-CT), although based on different methods, are nearly equivalent in performance and both are more accurate and faster than semiautomatic classification.more »
- Authors:
-
- Ernst-Moritz-Arndt Universitat Greifswald (Germany)
- Ernst-Moritz-Arndt Universitat Greifswald (Germany); Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Federal Research Institute for Animal Health, Island of Riems, Greifswald (Germany)
- Publication Date:
- Research Org.:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); German Science Foundation (DFG)
- OSTI Identifier:
- 1627669
- Grant/Contract Number:
- AC52-06NA25396; STA 1009/5-1
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PLoS ONE
- Additional Journal Information:
- Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 1932-6203
- Publisher:
- Public Library of Science
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; hidden Markov models; H5N1; BLAST algorithm; influenza A virus; phylogenetic analysis; sequence databases; animal phylogenetics; viral pathogens
Citation Formats
Van der Auwera, Sandra, Bulla, Ingo, Ziller, Mario, Pohlmann, Anne, Harder, Timm, and Stanke, Mario. ClassyFlu: Classification of Influenza A Viruses with Discriminatively Trained Profile-HMMs. United States: N. p., 2014.
Web. doi:10.1371/journal.pone.0084558.
Van der Auwera, Sandra, Bulla, Ingo, Ziller, Mario, Pohlmann, Anne, Harder, Timm, & Stanke, Mario. ClassyFlu: Classification of Influenza A Viruses with Discriminatively Trained Profile-HMMs. United States. https://doi.org/10.1371/journal.pone.0084558
Van der Auwera, Sandra, Bulla, Ingo, Ziller, Mario, Pohlmann, Anne, Harder, Timm, and Stanke, Mario. Fri .
"ClassyFlu: Classification of Influenza A Viruses with Discriminatively Trained Profile-HMMs". United States. https://doi.org/10.1371/journal.pone.0084558. https://www.osti.gov/servlets/purl/1627669.
@article{osti_1627669,
title = {ClassyFlu: Classification of Influenza A Viruses with Discriminatively Trained Profile-HMMs},
author = {Van der Auwera, Sandra and Bulla, Ingo and Ziller, Mario and Pohlmann, Anne and Harder, Timm and Stanke, Mario},
abstractNote = {Accurate and rapid characterization of influenza A virus (IAV) hemagglutinin (HA) and neuraminidase (NA) sequences with respect to subtype and clade is at the basis of extended diagnostic services and implicit to molecular epidemiologic studies. ClassyFlu is a new tool and web service for the classification of IAV sequences of the HA and NA gene into subtypes and phylogenetic clades using discriminatively trained profile hidden Markov models (HMMs), one for each subtype or clade. ClassyFlu merely requires as input unaligned, full-length or partial HA or NA DNA sequences. It enables rapid and highly accurate assignment of HA sequences to subtypes H1–H17 but particularly focusses on the finer grained assignment of sequences of highly pathogenic avian influenza viruses of subtype H5N1 according to the cladistics proposed by the H5N1 Evolution Working Group. NA sequences are classified into subtypes N1–N10. ClassyFlu was compared to semiautomatic classification approaches using BLAST and phylogenetics and additionally for H5 sequences to the new ‘‘Highly Pathogenic H5N1 Clade Classification Tool’’ (IRD-CT) proposed by the Influenza Research Database. Our results show that both web tools (ClassyFlu and IRD-CT), although based on different methods, are nearly equivalent in performance and both are more accurate and faster than semiautomatic classification. A retraining of ClassyFlu to altered cladistics as well as an extension of ClassyFlu to other IAV genome segments or fragments thereof is undemanding. This is exemplified by unambiguous assignment to a distinct cluster within subtype H7 of sequences of H7N9 viruses which emerged in China early in 2013 and caused more than 130 human infections.},
doi = {10.1371/journal.pone.0084558},
journal = {PLoS ONE},
number = 1,
volume = 9,
place = {United States},
year = {Fri Jan 03 00:00:00 EST 2014},
month = {Fri Jan 03 00:00:00 EST 2014}
}
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