Identification of probable genomic packaging signal sequence from SARS-CoV genome by bioinformatics analysis.
Identifieur interne : 003350 ( PubMed/Corpus ); précédent : 003349; suivant : 003351Identification of probable genomic packaging signal sequence from SARS-CoV genome by bioinformatics analysis.
Auteurs : Lei Qin ; Bin Xiong ; Cheng Luo ; Zong-Ming Guo ; Pei Hao ; Jiong Su ; Peng Nan ; Ying Feng ; Yi-Xiang Shi ; Xiao-Jing Yu ; Xiao-Min Luo ; Kai-Xian Chen ; Xu Shen ; Jian-Hua Shen ; Jian-Ping Zou ; Guo-Ping Zhao ; Tie-Liu Shi ; Wei-Zhong He ; Yang Zhong ; Hua-Liang Jiang ; Yi-Xue LiSource :
- Acta pharmacologica Sinica [ 1671-4083 ] ; 2003.
English descriptors
- KwdEn :
- Amino Acid Sequence, Base Sequence, Computational Biology, Coronavirus 229E, Human (genetics), Coronavirus, Bovine (genetics), Genome, Viral, Humans, Molecular Sequence Data, Murine hepatitis virus (genetics), Nucleocapsid Proteins (genetics), Protein Sorting Signals (genetics), Protein Structure, Secondary, RNA Interference, RNA, Antisense (genetics), RNA, Viral (genetics), SARS Virus (genetics), SARS Virus (isolation & purification), Sequence Alignment, Sequence Homology, Amino Acid, Severe Acute Respiratory Syndrome (virology), Viral Matrix Proteins (genetics).
- MESH :
- chemical , genetics : Nucleocapsid Proteins, Protein Sorting Signals, RNA, Antisense, RNA, Viral, Viral Matrix Proteins.
- genetics : Coronavirus 229E, Human, Coronavirus, Bovine, Murine hepatitis virus, SARS Virus.
- isolation & purification : SARS Virus.
- virology : Severe Acute Respiratory Syndrome.
- Amino Acid Sequence, Base Sequence, Computational Biology, Genome, Viral, Humans, Molecular Sequence Data, Protein Structure, Secondary, RNA Interference, Sequence Alignment, Sequence Homology, Amino Acid.
Abstract
To predict the probable genomic packaging signal of SARS-CoV by bioinformatics analysis. The derived packaging signal may be used to design antisense RNA and RNA interfere (RNAi) drugs treating SARS.
PubMed: 12791173
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Identification of probable genomic packaging signal sequence from SARS-CoV genome by bioinformatics analysis.</title><author><name sortKey="Qin, Lei" sort="Qin, Lei" uniqKey="Qin L" first="Lei" last="Qin">Lei Qin</name><affiliation><nlm:affiliation>Shanghai Center for Bioinformation Technology, Shanghai 201203, China.</nlm:affiliation></affiliation></author><author><name sortKey="Xiong, Bin" sort="Xiong, Bin" uniqKey="Xiong B" first="Bin" last="Xiong">Bin Xiong</name></author><author><name sortKey="Luo, Cheng" sort="Luo, Cheng" uniqKey="Luo C" first="Cheng" last="Luo">Cheng Luo</name></author><author><name sortKey="Guo, Zong Ming" sort="Guo, Zong Ming" uniqKey="Guo Z" first="Zong-Ming" last="Guo">Zong-Ming Guo</name></author><author><name sortKey="Hao, Pei" sort="Hao, Pei" uniqKey="Hao P" first="Pei" last="Hao">Pei Hao</name></author><author><name sortKey="Su, Jiong" sort="Su, Jiong" uniqKey="Su J" first="Jiong" last="Su">Jiong Su</name></author><author><name sortKey="Nan, Peng" sort="Nan, Peng" uniqKey="Nan P" first="Peng" last="Nan">Peng Nan</name></author><author><name sortKey="Feng, Ying" sort="Feng, Ying" uniqKey="Feng Y" first="Ying" last="Feng">Ying Feng</name></author><author><name sortKey="Shi, Yi Xiang" sort="Shi, Yi Xiang" uniqKey="Shi Y" first="Yi-Xiang" last="Shi">Yi-Xiang Shi</name></author><author><name sortKey="Yu, Xiao Jing" sort="Yu, Xiao Jing" uniqKey="Yu X" first="Xiao-Jing" last="Yu">Xiao-Jing Yu</name></author><author><name sortKey="Luo, Xiao Min" sort="Luo, Xiao Min" uniqKey="Luo X" first="Xiao-Min" last="Luo">Xiao-Min Luo</name></author><author><name sortKey="Chen, Kai Xian" sort="Chen, Kai Xian" uniqKey="Chen K" first="Kai-Xian" last="Chen">Kai-Xian Chen</name></author><author><name sortKey="Shen, Xu" sort="Shen, Xu" uniqKey="Shen X" first="Xu" last="Shen">Xu Shen</name></author><author><name sortKey="Shen, Jian Hua" sort="Shen, Jian Hua" uniqKey="Shen J" first="Jian-Hua" last="Shen">Jian-Hua Shen</name></author><author><name sortKey="Zou, Jian Ping" sort="Zou, Jian Ping" uniqKey="Zou J" first="Jian-Ping" last="Zou">Jian-Ping Zou</name></author><author><name sortKey="Zhao, Guo Ping" sort="Zhao, Guo Ping" uniqKey="Zhao G" first="Guo-Ping" last="Zhao">Guo-Ping Zhao</name></author><author><name sortKey="Shi, Tie Liu" sort="Shi, Tie Liu" uniqKey="Shi T" first="Tie-Liu" last="Shi">Tie-Liu Shi</name></author><author><name sortKey="He, Wei Zhong" sort="He, Wei Zhong" uniqKey="He W" first="Wei-Zhong" last="He">Wei-Zhong He</name></author><author><name sortKey="Zhong, Yang" sort="Zhong, Yang" uniqKey="Zhong Y" first="Yang" last="Zhong">Yang Zhong</name></author><author><name sortKey="Jiang, Hua Liang" sort="Jiang, Hua Liang" uniqKey="Jiang H" first="Hua-Liang" last="Jiang">Hua-Liang Jiang</name></author><author><name sortKey="Li, Yi Xue" sort="Li, Yi Xue" uniqKey="Li Y" first="Yi-Xue" last="Li">Yi-Xue Li</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2003">2003</date><idno type="RBID">pubmed:12791173</idno><idno type="pmid">12791173</idno><idno type="wicri:Area/PubMed/Corpus">003350</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">003350</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Identification of probable genomic packaging signal sequence from SARS-CoV genome by bioinformatics analysis.</title><author><name sortKey="Qin, Lei" sort="Qin, Lei" uniqKey="Qin L" first="Lei" last="Qin">Lei Qin</name><affiliation><nlm:affiliation>Shanghai Center for Bioinformation Technology, Shanghai 201203, China.</nlm:affiliation></affiliation></author><author><name sortKey="Xiong, Bin" sort="Xiong, Bin" uniqKey="Xiong B" first="Bin" last="Xiong">Bin Xiong</name></author><author><name sortKey="Luo, Cheng" sort="Luo, Cheng" uniqKey="Luo C" first="Cheng" last="Luo">Cheng Luo</name></author><author><name sortKey="Guo, Zong Ming" sort="Guo, Zong Ming" uniqKey="Guo Z" first="Zong-Ming" last="Guo">Zong-Ming Guo</name></author><author><name sortKey="Hao, Pei" sort="Hao, Pei" uniqKey="Hao P" first="Pei" last="Hao">Pei Hao</name></author><author><name sortKey="Su, Jiong" sort="Su, Jiong" uniqKey="Su J" first="Jiong" last="Su">Jiong Su</name></author><author><name sortKey="Nan, Peng" sort="Nan, Peng" uniqKey="Nan P" first="Peng" last="Nan">Peng Nan</name></author><author><name sortKey="Feng, Ying" sort="Feng, Ying" uniqKey="Feng Y" first="Ying" last="Feng">Ying Feng</name></author><author><name sortKey="Shi, Yi Xiang" sort="Shi, Yi Xiang" uniqKey="Shi Y" first="Yi-Xiang" last="Shi">Yi-Xiang Shi</name></author><author><name sortKey="Yu, Xiao Jing" sort="Yu, Xiao Jing" uniqKey="Yu X" first="Xiao-Jing" last="Yu">Xiao-Jing Yu</name></author><author><name sortKey="Luo, Xiao Min" sort="Luo, Xiao Min" uniqKey="Luo X" first="Xiao-Min" last="Luo">Xiao-Min Luo</name></author><author><name sortKey="Chen, Kai Xian" sort="Chen, Kai Xian" uniqKey="Chen K" first="Kai-Xian" last="Chen">Kai-Xian Chen</name></author><author><name sortKey="Shen, Xu" sort="Shen, Xu" uniqKey="Shen X" first="Xu" last="Shen">Xu Shen</name></author><author><name sortKey="Shen, Jian Hua" sort="Shen, Jian Hua" uniqKey="Shen J" first="Jian-Hua" last="Shen">Jian-Hua Shen</name></author><author><name sortKey="Zou, Jian Ping" sort="Zou, Jian Ping" uniqKey="Zou J" first="Jian-Ping" last="Zou">Jian-Ping Zou</name></author><author><name sortKey="Zhao, Guo Ping" sort="Zhao, Guo Ping" uniqKey="Zhao G" first="Guo-Ping" last="Zhao">Guo-Ping Zhao</name></author><author><name sortKey="Shi, Tie Liu" sort="Shi, Tie Liu" uniqKey="Shi T" first="Tie-Liu" last="Shi">Tie-Liu Shi</name></author><author><name sortKey="He, Wei Zhong" sort="He, Wei Zhong" uniqKey="He W" first="Wei-Zhong" last="He">Wei-Zhong He</name></author><author><name sortKey="Zhong, Yang" sort="Zhong, Yang" uniqKey="Zhong Y" first="Yang" last="Zhong">Yang Zhong</name></author><author><name sortKey="Jiang, Hua Liang" sort="Jiang, Hua Liang" uniqKey="Jiang H" first="Hua-Liang" last="Jiang">Hua-Liang Jiang</name></author><author><name sortKey="Li, Yi Xue" sort="Li, Yi Xue" uniqKey="Li Y" first="Yi-Xue" last="Li">Yi-Xue Li</name></author></analytic><series><title level="j">Acta pharmacologica Sinica</title><idno type="ISSN">1671-4083</idno><imprint><date when="2003" type="published">2003</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence</term><term>Base Sequence</term><term>Computational Biology</term><term>Coronavirus 229E, Human (genetics)</term><term>Coronavirus, Bovine (genetics)</term><term>Genome, Viral</term><term>Humans</term><term>Molecular Sequence Data</term><term>Murine hepatitis virus (genetics)</term><term>Nucleocapsid Proteins (genetics)</term><term>Protein Sorting Signals (genetics)</term><term>Protein Structure, Secondary</term><term>RNA Interference</term><term>RNA, Antisense (genetics)</term><term>RNA, Viral (genetics)</term><term>SARS Virus (genetics)</term><term>SARS Virus (isolation & purification)</term><term>Sequence Alignment</term><term>Sequence Homology, Amino Acid</term><term>Severe Acute Respiratory Syndrome (virology)</term><term>Viral Matrix Proteins (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Nucleocapsid Proteins</term><term>Protein Sorting Signals</term><term>RNA, Antisense</term><term>RNA, Viral</term><term>Viral Matrix Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Coronavirus 229E, Human</term><term>Coronavirus, Bovine</term><term>Murine hepatitis virus</term><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Severe Acute Respiratory Syndrome</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Base Sequence</term><term>Computational Biology</term><term>Genome, Viral</term><term>Humans</term><term>Molecular Sequence Data</term><term>Protein Structure, Secondary</term><term>RNA Interference</term><term>Sequence Alignment</term><term>Sequence Homology, Amino Acid</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">To predict the probable genomic packaging signal of SARS-CoV by bioinformatics analysis. The derived packaging signal may be used to design antisense RNA and RNA interfere (RNAi) drugs treating SARS.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">12791173</PMID><DateCompleted><Year>2004</Year><Month>03</Month><Day>22</Day></DateCompleted><DateRevised><Year>2006</Year><Month>11</Month><Day>15</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">1671-4083</ISSN><JournalIssue CitedMedium="Print"><Volume>24</Volume><Issue>6</Issue><PubDate><Year>2003</Year><Month>Jun</Month></PubDate></JournalIssue><Title>Acta pharmacologica Sinica</Title><ISOAbbreviation>Acta Pharmacol. Sin.</ISOAbbreviation></Journal><ArticleTitle>Identification of probable genomic packaging signal sequence from SARS-CoV genome by bioinformatics analysis.</ArticleTitle><Pagination><MedlinePgn>489-96</MedlinePgn></Pagination><Abstract><AbstractText Label="AIM" NlmCategory="OBJECTIVE">To predict the probable genomic packaging signal of SARS-CoV by bioinformatics analysis. The derived packaging signal may be used to design antisense RNA and RNA interfere (RNAi) drugs treating SARS.</AbstractText><AbstractText Label="METHODS" NlmCategory="METHODS">Based on the studies about the genomic packaging signals of MHV and BCoV, especially the information about primary and secondary structures, the putative genomic packaging signal of SARS-CoV were analyzed by using bioinformatic tools. Multi-alignment for the genomic sequences was performed among SARS-CoV, MHV, BCoV, PEDV and HCoV 229E. Secondary structures of RNA sequences were also predicted for the identification of the possible genomic packaging signals. Meanwhile, the N and M proteins of all five viruses were analyzed to study the evolutionary relationship with genomic packaging signals.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">The putative genomic packaging signal of SARS-CoV locates at the 3' end of ORF1b near that of MHV and BCoV, where is the most variable region of this gene. The RNA secondary structure of SARS-CoV genomic packaging signal is very similar to that of MHV and BCoV. The same result was also obtained in studying the genomic packaging signals of PEDV and HCoV 229E. Further more, the genomic sequence multi-alignment indicated that the locations of packaging signals of SARS-CoV, PEDV, and HCoV overlaped each other. It seems that the mutation rate of packaging signal sequences is much higher than the N protein, while only subtle variations for the M protein.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">The probable genomic packaging signal of SARS-CoV is analogous to that of MHV and BCoV, with the corresponding secondary RNA structure locating at the similar region of ORF1b. The positions where genomic packaging signals exist have suffered rounds of mutations, which may influence the primary structures of the N and M proteins consequently.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Qin</LastName><ForeName>Lei</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Shanghai Center for Bioinformation Technology, Shanghai 201203, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xiong</LastName><ForeName>Bin</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Luo</LastName><ForeName>Cheng</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Guo</LastName><ForeName>Zong-Ming</ForeName><Initials>ZM</Initials></Author><Author ValidYN="Y"><LastName>Hao</LastName><ForeName>Pei</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Su</LastName><ForeName>Jiong</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Nan</LastName><ForeName>Peng</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Feng</LastName><ForeName>Ying</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Shi</LastName><ForeName>Yi-Xiang</ForeName><Initials>YX</Initials></Author><Author ValidYN="Y"><LastName>Yu</LastName><ForeName>Xiao-Jing</ForeName><Initials>XJ</Initials></Author><Author ValidYN="Y"><LastName>Luo</LastName><ForeName>Xiao-Min</ForeName><Initials>XM</Initials></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Kai-Xian</ForeName><Initials>KX</Initials></Author><Author ValidYN="Y"><LastName>Shen</LastName><ForeName>Xu</ForeName><Initials>X</Initials></Author><Author ValidYN="Y"><LastName>Shen</LastName><ForeName>Jian-Hua</ForeName><Initials>JH</Initials></Author><Author ValidYN="Y"><LastName>Zou</LastName><ForeName>Jian-Ping</ForeName><Initials>JP</Initials></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Guo-Ping</ForeName><Initials>GP</Initials></Author><Author ValidYN="Y"><LastName>Shi</LastName><ForeName>Tie-Liu</ForeName><Initials>TL</Initials></Author><Author ValidYN="Y"><LastName>He</LastName><ForeName>Wei-Zhong</ForeName><Initials>WZ</Initials></Author><Author ValidYN="Y"><LastName>Zhong</LastName><ForeName>Yang</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Jiang</LastName><ForeName>Hua-Liang</ForeName><Initials>HL</Initials></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Yi-Xue</ForeName><Initials>YX</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Acta Pharmacol Sin</MedlineTA><NlmUniqueID>100956087</NlmUniqueID><ISSNLinking>1671-4083</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D019590">Nucleocapsid Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D021382">Protein Sorting Signals</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D016372">RNA, Antisense</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012367">RNA, Viral</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014763">Viral Matrix Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D028941" MajorTopicYN="N">Coronavirus 229E, Human</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017938" MajorTopicYN="N">Coronavirus, Bovine</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="N">Genome, Viral</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006517" MajorTopicYN="N">Murine hepatitis virus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019590" MajorTopicYN="N">Nucleocapsid Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D021382" MajorTopicYN="N">Protein Sorting Signals</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017433" MajorTopicYN="N">Protein Structure, Secondary</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D034622" MajorTopicYN="N">RNA Interference</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016372" MajorTopicYN="N">RNA, Antisense</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012367" MajorTopicYN="N">RNA, Viral</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D045473" MajorTopicYN="N">SARS Virus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016415" MajorTopicYN="N">Sequence Alignment</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017386" MajorTopicYN="N">Sequence Homology, Amino Acid</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D045169" MajorTopicYN="N">Severe Acute Respiratory Syndrome</DescriptorName><QualifierName UI="Q000821" MajorTopicYN="Y">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014763" MajorTopicYN="N">Viral Matrix Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2003</Year><Month>6</Month><Day>7</Day><Hour>5</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2004</Year><Month>3</Month><Day>23</Day><Hour>5</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2003</Year><Month>6</Month><Day>7</Day><Hour>5</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">12791173</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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