ZCURVE_CoV: a new system to recognize protein coding genes in coronavirus genomes, and its applications in analyzing SARS-CoV genomes
Identifieur interne : 000E29 ( Pmc/Curation ); précédent : 000E28; suivant : 000E30ZCURVE_CoV: a new system to recognize protein coding genes in coronavirus genomes, and its applications in analyzing SARS-CoV genomes
Auteurs : Ling-Ling Chen [République populaire de Chine] ; Hong-Yu Ou [République populaire de Chine] ; Ren Zhang [République populaire de Chine] ; Chun-Ting Zhang [République populaire de Chine]Source :
- Biochemical and Biophysical Research Communications [ 0006-291X ] ; 2003.
Abstract
A new system to recognize protein coding genes in the coronavirus genomes, specially suitable for the SARS-CoV genomes, has been proposed in this paper. Compared with some existing systems, the new program package has the merits of simplicity, high accuracy, reliability, and quickness. The system ZCURVE_CoV has been run for each of the 11 newly sequenced SARS-CoV genomes. Consequently, six genomes not annotated previously have been annotated, and some problems of previous annotations in the remaining five genomes have been pointed out and discussed. In addition to the polyprotein chain ORFs 1a and 1b and the four genes coding for the major structural proteins, spike (S), small envelop (E), membrane (M), and nuleocaspid (N), respectively, ZCURVE_CoV also predicts 5–6 putative proteins in length between 39 and 274 amino acids with unknown functions. Some single nucleotide mutations within these putative coding sequences have been detected and their biological implications are discussed. A web service is provided, by which a user can obtain the annotated result immediately by pasting the SARS-CoV genome sequences into the input window on the web site (
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DOI: 10.1016/S0006-291X(03)01192-6
PubMed: 12859968
PubMed Central: 7134609
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xml:lang="en" level="a" type="main">ZCURVE_CoV: a new system to recognize protein coding genes in coronavirus genomes, and its applications in analyzing SARS-CoV genomes</title><author><name sortKey="Chen, Ling Ling" sort="Chen, Ling Ling" uniqKey="Chen L" first="Ling-Ling" last="Chen">Ling-Ling Chen</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Department of Physics, Tianjin University, Tianjin 300072, PR China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Physics, Tianjin University, Tianjin 300072</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF2">Department of Biology, Shandong University of Technology, Zibo 255049, PR China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Biology, Shandong University of Technology, Zibo 255049</wicri:regionArea></affiliation></author><author><name sortKey="Ou, Hong Yu" sort="Ou, Hong Yu" uniqKey="Ou H" first="Hong-Yu" last="Ou">Hong-Yu Ou</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Department of Physics, Tianjin University, Tianjin 300072, PR China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Physics, Tianjin University, Tianjin 300072</wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Ren" sort="Zhang, Ren" uniqKey="Zhang R" first="Ren" last="Zhang">Ren Zhang</name><affiliation wicri:level="1"><nlm:aff id="AFF3">Department of Epidemiology and Biostatistics, Tianjin Cancer Institute and Hospital, Tianjin 300060, PR China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Epidemiology and Biostatistics, Tianjin Cancer Institute and Hospital, Tianjin 300060</wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Chun Ting" sort="Zhang, Chun Ting" uniqKey="Zhang C" first="Chun-Ting" last="Zhang">Chun-Ting Zhang</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Department of Physics, Tianjin University, Tianjin 300072, PR China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Physics, Tianjin University, Tianjin 300072</wicri:regionArea></affiliation></author></analytic><series><title level="j">Biochemical and Biophysical Research Communications</title><idno type="ISSN">0006-291X</idno><idno type="eISSN">1090-2104</idno><imprint><date when="2003">2003</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>A new system to recognize protein coding genes in the coronavirus genomes, specially suitable for the SARS-CoV genomes, has been proposed in this paper. Compared with some existing systems, the new program package has the merits of simplicity, high accuracy, reliability, and quickness. The system ZCURVE_CoV has been run for each of the 11 newly sequenced SARS-CoV genomes. Consequently, six genomes not annotated previously have been annotated, and some problems of previous annotations in the remaining five genomes have been pointed out and discussed. In addition to the polyprotein chain ORFs 1a and 1b and the four genes coding for the major structural proteins, spike (S), small envelop (E), membrane (M), and nuleocaspid (N), respectively, ZCURVE_CoV also predicts 5–6 putative proteins in length between 39 and 274 amino acids with unknown functions. Some single nucleotide mutations within these putative coding sequences have been detected and their biological implications are discussed. A web service is provided, by which a user can obtain the annotated result immediately by pasting the SARS-CoV genome sequences into the input window on the web site (<ext-link ext-link-type="uri" xlink:href="http://tubic.tju.edu.cn/sars/">http://tubic.tju.edu.cn/sars/</ext-link>). The software ZCURVE_CoV can also be downloaded freely from the web address mentioned above and run in computers under the platforms of Windows or Linux.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Peiris, J S" uniqKey="Peiris J">J.S. Peiris</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ksiazek, T G" uniqKey="Ksiazek T">T.G. Ksiazek</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Drosten, C" uniqKey="Drosten C">C. Drosten</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tsang, K W" uniqKey="Tsang K">K.W. Tsang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lee, N" uniqKey="Lee N">N. Lee</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Poutanen, S M" uniqKey="Poutanen S">S.M. Poutanen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rota, P A" uniqKey="Rota P">P.A. Rota</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Marra, M A" uniqKey="Marra M">M.A. Marra</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Qin, E" uniqKey="Qin E">E’d. Qin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Besemer, J" uniqKey="Besemer J">J. Besemer</name></author><author><name sortKey="Borodovsky, M" uniqKey="Borodovsky M">M. Borodovsky</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Salzberg, S L" uniqKey="Salzberg S">S.L. Salzberg</name></author><author><name sortKey="Delcher, A L" uniqKey="Delcher A">A.L. Delcher</name></author><author><name sortKey="Kasif, S" uniqKey="Kasif S">S. Kasif</name></author><author><name sortKey="White, O" uniqKey="White O">O. White</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Guo, F B" uniqKey="Guo F">F.B. Guo</name></author><author><name sortKey="Ou, H Y" uniqKey="Ou H">H.Y. Ou</name></author><author><name sortKey="Zhang, C T" uniqKey="Zhang C">C.-T. Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, C T" uniqKey="Zhang C">C.-T. Zhang</name></author><author><name sortKey="Zhang, R" uniqKey="Zhang R">R. Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, C T" uniqKey="Zhang C">C.-T. Zhang</name></author><author><name sortKey="Wang, J" uniqKey="Wang J">J. Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jenkins, G M" uniqKey="Jenkins G">G.M. Jenkins</name></author><author><name sortKey="Holmes, E C" uniqKey="Holmes E">E.C. Holmes</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ziebuhr, J" uniqKey="Ziebuhr J">J. Ziebuhr</name></author><author><name sortKey="Snijder, E J" uniqKey="Snijder E">E.J. Snijder</name></author><author><name sortKey="Gorbalenya, A E" uniqKey="Gorbalenya A">A.E. Gorbalenya</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thompson, J D" uniqKey="Thompson J">J.D. Thompson</name></author><author><name sortKey="Higgins, D G" uniqKey="Higgins D">D.G. Higgins</name></author><author><name sortKey="Gibson, T J" uniqKey="Gibson T">T.J. Gibson</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Biochem Biophys Res Commun</journal-id><journal-id journal-id-type="iso-abbrev">Biochem. Biophys. Res. Commun</journal-id><journal-title-group><journal-title>Biochemical and Biophysical Research Communications</journal-title></journal-title-group><issn pub-type="ppub">0006-291X</issn><issn pub-type="epub">1090-2104</issn><publisher><publisher-name>Elsevier Science (USA).</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">12859968</article-id><article-id pub-id-type="pmc">7134609</article-id><article-id pub-id-type="publisher-id">S0006-291X(03)01192-6</article-id><article-id pub-id-type="doi">10.1016/S0006-291X(03)01192-6</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>ZCURVE_CoV: a new system to recognize protein coding genes in coronavirus genomes, and its applications in analyzing SARS-CoV genomes</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Chen</surname><given-names>Ling-Ling</given-names></name><xref rid="AFF1" ref-type="aff">a</xref><xref rid="AFF2" ref-type="aff">b</xref><xref rid="FN1" ref-type="fn">1</xref></contrib><contrib contrib-type="author"><name><surname>Ou</surname><given-names>Hong-Yu</given-names></name><xref rid="AFF1" ref-type="aff">a</xref><xref rid="FN1" ref-type="fn">1</xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Ren</given-names></name><xref rid="AFF3" ref-type="aff">c</xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Chun-Ting</given-names></name><email>ctzhang@tju.edu.cn</email><xref rid="AFF1" ref-type="aff">a</xref><xref rid="COR1" ref-type="corresp">∗</xref></contrib></contrib-group><aff id="AFF1"><label>a</label>Department of Physics, Tianjin University, Tianjin 300072, PR China</aff><aff id="AFF2"><label>b</label>Department of Biology, Shandong University of Technology, Zibo 255049, PR China</aff><aff id="AFF3"><label>c</label>Department of Epidemiology and Biostatistics, Tianjin Cancer Institute and Hospital, Tianjin 300060, PR China</aff><author-notes><corresp id="COR1"><label>∗</label>Corresponding author. Fax: +86-22-2740-2697 <email>ctzhang@tju.edu.cn</email></corresp><fn id="FN1"><label>1</label><p>These authors contributed equally to this work.</p></fn></author-notes><pub-date pub-type="pmc-release"><day>27</day><month>6</month><year>2003</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on .</pmc-comment>
<pub-date pub-type="ppub"><day>25</day><month>7</month><year>2003</year></pub-date><pub-date pub-type="epub"><day>27</day><month>6</month><year>2003</year></pub-date><volume>307</volume><issue>2</issue><fpage>382</fpage><lpage>388</lpage><history><date date-type="received"><day>23</day><month>5</month><year>2003</year></date></history><permissions><copyright-statement>Copyright © 2003 Elsevier Science (USA). All rights reserved.</copyright-statement><copyright-year>2003</copyright-year><copyright-holder>Elsevier Science (USA)</copyright-holder><license><license-p>Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.</license-p></license></permissions><abstract><p>A new system to recognize protein coding genes in the coronavirus genomes, specially suitable for the SARS-CoV genomes, has been proposed in this paper. Compared with some existing systems, the new program package has the merits of simplicity, high accuracy, reliability, and quickness. The system ZCURVE_CoV has been run for each of the 11 newly sequenced SARS-CoV genomes. Consequently, six genomes not annotated previously have been annotated, and some problems of previous annotations in the remaining five genomes have been pointed out and discussed. In addition to the polyprotein chain ORFs 1a and 1b and the four genes coding for the major structural proteins, spike (S), small envelop (E), membrane (M), and nuleocaspid (N), respectively, ZCURVE_CoV also predicts 5–6 putative proteins in length between 39 and 274 amino acids with unknown functions. Some single nucleotide mutations within these putative coding sequences have been detected and their biological implications are discussed. A web service is provided, by which a user can obtain the annotated result immediately by pasting the SARS-CoV genome sequences into the input window on the web site (<ext-link ext-link-type="uri" xlink:href="http://tubic.tju.edu.cn/sars/">http://tubic.tju.edu.cn/sars/</ext-link>). The software ZCURVE_CoV can also be downloaded freely from the web address mentioned above and run in computers under the platforms of Windows or Linux.</p></abstract><kwd-group><title>Keywords</title><kwd>Coronavirus</kwd><kwd>Severe acute respiratory syndrome</kwd><kwd>SARS-CoV</kwd><kwd>Genome</kwd><kwd>Gene-finding</kwd><kwd>Mutation</kwd></kwd-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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