ClassyFlu: classification of influenza A viruses with Discriminatively trained profile-HMMs.

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 classi...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Sandra Van der Auwera, Ingo Bulla, Mario Ziller, Anne Pohlmann, Timm Harder, Mario Stanke
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/db53bf2324ce4aa9850d5469777e25aa
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:db53bf2324ce4aa9850d5469777e25aa
record_format	dspace
spelling	oai:doaj.org-article:db53bf2324ce4aa9850d5469777e25aa2021-11-18T08:38:57ZClassyFlu: classification of influenza A viruses with Discriminatively trained profile-HMMs.1932-620310.1371/journal.pone.0084558https://doaj.org/article/db53bf2324ce4aa9850d5469777e25aa2014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24404173/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Accurate 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. http://bioinf.uni-greifswald.de/ClassyFlu is a free web service. For local execution, the ClassyFlu source code in PERL is freely available.Sandra Van der AuweraIngo BullaMario ZillerAnne PohlmannTimm HarderMario StankePublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 1, p e84558 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Sandra Van der Auwera Ingo Bulla Mario Ziller Anne Pohlmann Timm Harder Mario Stanke ClassyFlu: classification of influenza A viruses with Discriminatively trained profile-HMMs.
description	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. http://bioinf.uni-greifswald.de/ClassyFlu is a free web service. For local execution, the ClassyFlu source code in PERL is freely available.
format	article
author	Sandra Van der Auwera Ingo Bulla Mario Ziller Anne Pohlmann Timm Harder Mario Stanke
author_facet	Sandra Van der Auwera Ingo Bulla Mario Ziller Anne Pohlmann Timm Harder Mario Stanke
author_sort	Sandra Van der Auwera
title	ClassyFlu: classification of influenza A viruses with Discriminatively trained profile-HMMs.
title_short	ClassyFlu: classification of influenza A viruses with Discriminatively trained profile-HMMs.
title_full	ClassyFlu: classification of influenza A viruses with Discriminatively trained profile-HMMs.
title_fullStr	ClassyFlu: classification of influenza A viruses with Discriminatively trained profile-HMMs.
title_full_unstemmed	ClassyFlu: classification of influenza A viruses with Discriminatively trained profile-HMMs.
title_sort	classyflu: classification of influenza a viruses with discriminatively trained profile-hmms.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/db53bf2324ce4aa9850d5469777e25aa
work_keys_str_mv	AT sandravanderauwera classyfluclassificationofinfluenzaaviruseswithdiscriminativelytrainedprofilehmms AT ingobulla classyfluclassificationofinfluenzaaviruseswithdiscriminativelytrainedprofilehmms AT marioziller classyfluclassificationofinfluenzaaviruseswithdiscriminativelytrainedprofilehmms AT annepohlmann classyfluclassificationofinfluenzaaviruseswithdiscriminativelytrainedprofilehmms AT timmharder classyfluclassificationofinfluenzaaviruseswithdiscriminativelytrainedprofilehmms AT mariostanke classyfluclassificationofinfluenzaaviruseswithdiscriminativelytrainedprofilehmms
_version_	1718421531260878848

ClassyFlu: classification of influenza A viruses with Discriminatively trained profile-HMMs.

Ejemplares similares