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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
KeywordsConvergent evolution
Factor analysis
Horizontal gene transfer
RNA virus
SARS
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
2020 Impact Factor: 3.169
2020 SCImago Journal Rankings: 1.567
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.subjectConvergent evolution-
dc.subjectFactor analysis-
dc.subjectHorizontal gene transfer-
dc.subjectRNA virus-
dc.subjectSARS-
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-
dc.identifier.issnl1471-2105-

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