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Article: Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling

TitleRelationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling
Authors
Issue Date2003
PublisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcbioinformatics/
Citation
B M C Bioinformatics, 2003, v. 4 n. 1, p. 43 How to Cite?
AbstractBACKGROUND: The exact origin of the cause of the Severe Acute Respiratory Syndrome (SARS) is still an open question. The genomic sequence relationship of SARS-CoV with 30 different single-stranded RNA (ssRNA) viruses of various families was studied using two non-standard approaches. Both approaches began with the vectorial profiling of the tetra-nucleotide usage pattern V for each virus. In approach one, a distance measure of a vector V, based on correlation coefficient was devised to construct a relationship tree by the neighbor-joining algorithm. In approach two, a multivariate factor analysis was performed to derive the embedded tetra-nucleotide usage patterns. These patterns were subsequently used to classify the selected viruses. RESULTS: Both approaches yielded relationship outcomes that are consistent with the known virus classification. They also indicated that the genome of RNA viruses from the same family conform to a specific pattern of word usage. Based on the correlation of the overall tetra-nucleotide usage patterns, the Transmissible Gastroenteritis Virus (TGV) and the Feline CoronaVirus (FCoV) are closest to SARS-CoV. Surprisingly also, the RNA viruses that do not go through a DNA stage displayed a remarkable discrimination against the CpG and UpA di-nucleotide (z = -77.31, -52.48 respectively) and selection for UpG and CpA (z = 65.79,49.99 respectively). Potential factors influencing these biases are discussed. CONCLUSION: The study of genomic word usage is a powerful method to classify RNA viruses. The congruence of the relationship outcomes with the known classification indicates that there exist phylogenetic signals in the tetra-nucleotide usage patterns, that is most prominent in the replicase open reading frames.
Persistent Identifierhttp://hdl.handle.net/10722/45200
ISSN
2015 Impact Factor: 2.435
2015 SCImago Journal Rankings: 1.722
PubMed Central ID
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorYap, YLen_HK
dc.contributor.authorZhang, XWen_HK
dc.contributor.authorDanchin, ALMen_HK
dc.date.accessioned2007-10-30T06:19:37Z-
dc.date.available2007-10-30T06:19:37Z-
dc.date.issued2003en_HK
dc.identifier.citationB M C Bioinformatics, 2003, v. 4 n. 1, p. 43en_HK
dc.identifier.issn1471-2105en_HK
dc.identifier.urihttp://hdl.handle.net/10722/45200-
dc.description.abstractBACKGROUND: The exact origin of the cause of the Severe Acute Respiratory Syndrome (SARS) is still an open question. The genomic sequence relationship of SARS-CoV with 30 different single-stranded RNA (ssRNA) viruses of various families was studied using two non-standard approaches. Both approaches began with the vectorial profiling of the tetra-nucleotide usage pattern V for each virus. In approach one, a distance measure of a vector V, based on correlation coefficient was devised to construct a relationship tree by the neighbor-joining algorithm. In approach two, a multivariate factor analysis was performed to derive the embedded tetra-nucleotide usage patterns. These patterns were subsequently used to classify the selected viruses. RESULTS: Both approaches yielded relationship outcomes that are consistent with the known virus classification. They also indicated that the genome of RNA viruses from the same family conform to a specific pattern of word usage. Based on the correlation of the overall tetra-nucleotide usage patterns, the Transmissible Gastroenteritis Virus (TGV) and the Feline CoronaVirus (FCoV) are closest to SARS-CoV. Surprisingly also, the RNA viruses that do not go through a DNA stage displayed a remarkable discrimination against the CpG and UpA di-nucleotide (z = -77.31, -52.48 respectively) and selection for UpG and CpA (z = 65.79,49.99 respectively). Potential factors influencing these biases are discussed. CONCLUSION: The study of genomic word usage is a powerful method to classify RNA viruses. The congruence of the relationship outcomes with the known classification indicates that there exist phylogenetic signals in the tetra-nucleotide usage patterns, that is most prominent in the replicase open reading frames.en_HK
dc.format.extent710866 bytes-
dc.format.extent2104 bytes-
dc.format.mimetypeapplication/pdf-
dc.format.mimetypetext/plain-
dc.languageengen_HK
dc.publisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcbioinformatics/en_HK
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.subject.meshGene Expression Profiling - methods - statistics & numerical dataen_HK
dc.subject.meshGene Expression Regulation, Viral - geneticsen_HK
dc.subject.meshMicrosatellite Repeats - geneticsen_HK
dc.subject.meshRNA Viruses - genetics - pathogenicityen_HK
dc.subject.meshSARS Virus - genetics - pathogenicityen_HK
dc.titleRelationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profilingen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1471-2105&volume=4&issue=1&spage=43&epage=&date=2003&atitle=Relationship+of+SARS-CoV+to+other+pathogenic+RNA+viruses+explored+by+tetranucleotide+usage+profilingen_HK
dc.description.naturepublished_or_final_versionen_HK
dc.identifier.doi10.1186/1471-2105-4-43en_HK
dc.identifier.pmid14499005-
dc.identifier.pmcidPMC222961-
dc.identifier.scopuseid_2-s2.0-0642367621-
dc.identifier.hkuros95395-
dc.identifier.isiWOS:000186342100001-
dc.identifier.citeulike10742232-

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