Please use this identifier to cite or link to this item: https://doi.org/10.1371/journal.pone.0086921
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dc.titleLABEL: Fast and accurate lineage assignment with assessment of H5N1 and H9N2 influenza A hemagglutinins
dc.contributor.authorShepard, S.S.
dc.contributor.authorDavis, C.T.
dc.contributor.authorBahl, J.
dc.contributor.authorRivailler, P.
dc.contributor.authorYork, I.A.
dc.contributor.authorDonis, R.O.
dc.date.accessioned2016-09-06T03:00:08Z
dc.date.available2016-09-06T03:00:08Z
dc.date.issued2014-01-23
dc.identifier.citationShepard, S.S., Davis, C.T., Bahl, J., Rivailler, P., York, I.A., Donis, R.O. (2014-01-23). LABEL: Fast and accurate lineage assignment with assessment of H5N1 and H9N2 influenza A hemagglutinins. PLoS ONE 9 (1) : -. ScholarBank@NUS Repository. https://doi.org/10.1371/journal.pone.0086921
dc.identifier.issn19326203
dc.identifier.urihttp://scholarbank.nus.edu.sg/handle/10635/126509
dc.description.abstractThe evolutionary classification of influenza genes into lineages is a first step in understanding their molecular epidemiology and can inform the subsequent implementation of control measures. We introduce a novel approach called Lineage Assignment By Extended Learning (LABEL) to rapidly determine cladistic information for any number of genes without the need for time-consuming sequence alignment, phylogenetic tree construction, or manual annotation. Instead, LABEL relies on hidden Markov model profiles and support vector machine training to hierarchically classify gene sequences by their similarity to pre-defined lineages. We assessed LABEL by analyzing the annotated hemagglutinin genes of highly pathogenic (H5N1) and low pathogenicity (H9N2) avian influenza A viruses. Using the WHO/FAO/OIE H5N1 evolution working group nomenclature, the LABEL pipeline quickly and accurately identified the H5 lineages of uncharacterized sequences. Moreover, we developed an updated clade nomenclature for the H9 hemagglutinin gene and show a similarly fast and reliable phylogenetic assessment with LABEL. While this study was focused on hemagglutinin sequences, LABEL could be applied to the analysis of any gene and shows great potential to guide molecular epidemiology activities, accelerate database annotation, and provide a data sorting tool for other large-scale bioinformatic studies.
dc.description.urihttp://libproxy1.nus.edu.sg/login?url=http://dx.doi.org/10.1371/journal.pone.0086921
dc.sourceScopus
dc.typeArticle
dc.contributor.departmentDUKE-NUS GRADUATE MEDICAL SCHOOL S'PORE
dc.description.doi10.1371/journal.pone.0086921
dc.description.sourcetitlePLoS ONE
dc.description.volume9
dc.description.issue1
dc.description.page-
dc.description.codenPOLNC
dc.identifier.isiut000330288000172
dc.published.statePublished
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