Comparative studies of alignment, alignment-free and SVM based approaches for predicting the hosts of viruses based on viral sequences
Identifieur interne : 000A40 ( Main/Merge ); précédent : 000A39; suivant : 000A41Comparative studies of alignment, alignment-free and SVM based approaches for predicting the hosts of viruses based on viral sequences
Auteurs : Han Li [États-Unis] ; Fengzhu Sun [États-Unis, République populaire de Chine]Source :
- Scientific Reports [ 2045-2322 ] ; 2018.
Descripteurs français
- KwdFr :
- ADN viral (analyse), Alignement de séquences (), Analyse de séquence d'ADN (), Coronavirus (génétique), Coronavirus du syndrome respiratoire du Moyen-Orient (génétique), Glycoprotéine de spicule des coronavirus (génétique), Génome viral (génétique), Machine à vecteur de support, Modèles théoriques, Pandémies, Phylogénie, Virus de la grippe A (génétique), Virus de la rage (génétique).
- MESH :
- analyse : ADN viral.
- génétique : Coronavirus, Coronavirus du syndrome respiratoire du Moyen-Orient, Glycoprotéine de spicule des coronavirus, Génome viral, Virus de la grippe A, Virus de la rage.
- Alignement de séquences, Analyse de séquence d'ADN, Machine à vecteur de support, Modèles théoriques, Pandémies, Phylogénie.
English descriptors
- KwdEn :
- Coronavirus (genetics), DNA, Viral (analysis), Genome, Viral (genetics), Host Microbial Interactions (genetics), Host Microbial Interactions (physiology), Influenza A virus (genetics), Middle East Respiratory Syndrome Coronavirus (genetics), Models, Theoretical, Pandemics, Phylogeny, Rabies virus (genetics), Sequence Alignment (methods), Sequence Analysis, DNA (methods), Spike Glycoprotein, Coronavirus (genetics), Support Vector Machine.
- MESH :
- chemical , analysis : DNA, Viral.
- genetics : Coronavirus, Genome, Viral, Host Microbial Interactions, Influenza A virus, Middle East Respiratory Syndrome Coronavirus, Rabies virus, Spike Glycoprotein, Coronavirus.
- methods : Sequence Alignment, Sequence Analysis, DNA.
- physiology : Host Microbial Interactions.
- Models, Theoretical, Pandemics, Phylogeny, Support Vector Machine.
Abstract
Predicting the hosts of newly discovered viruses is important for pandemic surveillance of infectious diseases. We investigated the use of alignment-based and alignment-free methods and support vector machine using mononucleotide frequency and dinucleotide bias to predict the hosts of viruses, and applied these approaches to three datasets: rabies virus, coronavirus, and influenza A virus. For coronavirus, we used the spike gene sequences, while for rabies and influenza A viruses, we used the more conserved nucleoprotein gene sequences. We compared the three methods under different scenarios and showed that their performances are highly correlated with the variability of sequences and sample size. For conserved genes like the nucleoprotein gene, longer
Url:
DOI: 10.1038/s41598-018-28308-x
PubMed: 29968780
PubMed Central: 6030160
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PMC:6030160Le document en format XML
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<term>DNA, Viral (analysis)</term>
<term>Genome, Viral (genetics)</term>
<term>Host Microbial Interactions (genetics)</term>
<term>Host Microbial Interactions (physiology)</term>
<term>Influenza A virus (genetics)</term>
<term>Middle East Respiratory Syndrome Coronavirus (genetics)</term>
<term>Models, Theoretical</term>
<term>Pandemics</term>
<term>Phylogeny</term>
<term>Rabies virus (genetics)</term>
<term>Sequence Alignment (methods)</term>
<term>Sequence Analysis, DNA (methods)</term>
<term>Spike Glycoprotein, Coronavirus (genetics)</term>
<term>Support Vector Machine</term>
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<term>Alignement de séquences ()</term>
<term>Analyse de séquence d'ADN ()</term>
<term>Coronavirus (génétique)</term>
<term>Coronavirus du syndrome respiratoire du Moyen-Orient (génétique)</term>
<term>Glycoprotéine de spicule des coronavirus (génétique)</term>
<term>Génome viral (génétique)</term>
<term>Machine à vecteur de support</term>
<term>Modèles théoriques</term>
<term>Pandémies</term>
<term>Phylogénie</term>
<term>Virus de la grippe A (génétique)</term>
<term>Virus de la rage (génétique)</term>
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<term>Genome, Viral</term>
<term>Host Microbial Interactions</term>
<term>Influenza A virus</term>
<term>Middle East Respiratory Syndrome Coronavirus</term>
<term>Rabies virus</term>
<term>Spike Glycoprotein, Coronavirus</term>
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<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Coronavirus</term>
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<term>Glycoprotéine de spicule des coronavirus</term>
<term>Génome viral</term>
<term>Virus de la grippe A</term>
<term>Virus de la rage</term>
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<front><div type="abstract" xml:lang="en"><p id="Par1">Predicting the hosts of newly discovered viruses is important for pandemic surveillance of infectious diseases. We investigated the use of alignment-based and alignment-free methods and support vector machine using mononucleotide frequency and dinucleotide bias to predict the hosts of viruses, and applied these approaches to three datasets: rabies virus, coronavirus, and influenza A virus. For coronavirus, we used the spike gene sequences, while for rabies and influenza A viruses, we used the more conserved nucleoprotein gene sequences. We compared the three methods under different scenarios and showed that their performances are highly correlated with the variability of sequences and sample size. For conserved genes like the nucleoprotein gene, longer <italic>k</italic>
-mers than mono- and dinucleotides are needed to better distinguish the sequences. We also showed that both alignment-based and alignment-free methods can accurately predict the hosts of viruses. When alignment is difficult to achieve or highly time-consuming, alignment-free methods can be a promising substitute to predict the hosts of new viruses.</p>
</div>
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