Palindromes in SARS and Other Coronaviruses
Identifieur interne : 001576 ( Pmc/Checkpoint ); précédent : 001575; suivant : 001577Palindromes in SARS and Other Coronaviruses
Auteurs : David S. H. Chew ; Kwok Pui Choi ; Hans Heidner ; Ming-Ying LeungSource :
- INFORMS journal on computing [ 1091-9856 ] ; 2004.
Abstract
With the identification of a novel coronavirus associated with the
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PubMed: 24966663
PubMed Central: 4066412
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Palindromes in SARS and Other Coronaviruses</title><author><name sortKey="Chew, David S H" sort="Chew, David S H" uniqKey="Chew D" first="David S. H." last="Chew">David S. H. Chew</name></author><author><name sortKey="Choi, Kwok Pui" sort="Choi, Kwok Pui" uniqKey="Choi K" first="Kwok Pui" last="Choi">Kwok Pui Choi</name></author><author><name sortKey="Heidner, Hans" sort="Heidner, Hans" uniqKey="Heidner H" first="Hans" last="Heidner">Hans Heidner</name></author><author><name sortKey="Leung, Ming Ying" sort="Leung, Ming Ying" uniqKey="Leung M" first="Ming-Ying" last="Leung">Ming-Ying Leung</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24966663</idno><idno type="pmc">4066412</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4066412</idno><idno type="RBID">PMC:4066412</idno><date when="2004">2004</date><idno type="wicri:Area/Pmc/Corpus">000D33</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000D33</idno><idno type="wicri:Area/Pmc/Curation">000D33</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000D33</idno><idno type="wicri:Area/Pmc/Checkpoint">001576</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001576</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Palindromes in SARS and Other Coronaviruses</title><author><name sortKey="Chew, David S H" sort="Chew, David S H" uniqKey="Chew D" first="David S. H." last="Chew">David S. H. Chew</name></author><author><name sortKey="Choi, Kwok Pui" sort="Choi, Kwok Pui" uniqKey="Choi K" first="Kwok Pui" last="Choi">Kwok Pui Choi</name></author><author><name sortKey="Heidner, Hans" sort="Heidner, Hans" uniqKey="Heidner H" first="Hans" last="Heidner">Hans Heidner</name></author><author><name sortKey="Leung, Ming Ying" sort="Leung, Ming Ying" uniqKey="Leung M" first="Ming-Ying" last="Leung">Ming-Ying Leung</name></author></analytic><series><title level="j">INFORMS journal on computing</title><idno type="ISSN">1091-9856</idno><imprint><date when="2004">2004</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="P1">With the identification of a novel coronavirus associated with the <italic>severe acute respiratory syndrome</italic> (SARS), computational analysis of its RNA genome sequence is expected to give useful clues to help elucidate the origin, evolution, and pathogenicity of the virus. In this paper, we study the collective counts of palindromes in the SARS genome along with all the completely sequenced coronaviruses. Based on a Markov-chain model for the genome sequence, the mean and standard deviation for the number of palindromes at or above a given length are derived. These theoretical results are complemented by extensive simulations to provide empirical estimates. Using a <italic>z</italic> score obtained from these mathematical and empirical means and standard deviations, we have observed that palindromes of length four are significantly underrepresented in all the coronaviruses in our data set. In contrast, length-six palindromes are significantly underrepresented only in the SARS coronavirus. Two other features are unique to the SARS sequence. First, there is a length-22 palindrome TCTTTAACAAGCTTGTTAAAGA spanning positions 25962–25983. Second, there are two repeating length-12 palindromes TTATAATTATAA spanning positions 22712–22723 and 22796–22807. Some further investigations into possible biological implications of these palindrome features are proposed.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<pmc-dir>properties manuscript</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-journal-id">101531948</journal-id><journal-id journal-id-type="pubmed-jr-id">37727</journal-id><journal-id journal-id-type="nlm-ta">INFORMS J Comput</journal-id><journal-id journal-id-type="iso-abbrev">INFORMS J Comput</journal-id><journal-title-group><journal-title>INFORMS journal on computing</journal-title></journal-title-group><issn pub-type="ppub">1091-9856</issn></journal-meta><article-meta><article-id pub-id-type="pmid">24966663</article-id><article-id pub-id-type="pmc">4066412</article-id><article-id pub-id-type="manuscript">NIHMS583805</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Palindromes in SARS and Other Coronaviruses</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Chew</surname><given-names>David S. H.</given-names></name><aff id="A1">Department of Mathematics, National University of Singapore, Singapore 117543, Singapore</aff><email>matchewd@nus.edu.sg</email></contrib><contrib contrib-type="author"><name><surname>Choi</surname><given-names>Kwok Pui</given-names></name><aff id="A2">Departments of Mathematics, and of Statistics and Applied Probability, National University of Singapore, Singapore 117543, Singapore</aff><email>matckp@nus.edu.sg</email></contrib><contrib contrib-type="author"><name><surname>Heidner</surname><given-names>Hans</given-names></name><aff id="A3">Department of Biology, University of Texas at San Antonio, San Antonio, Texas 78249, USA</aff><email>hheidner@utsa.edu</email></contrib><contrib contrib-type="author"><name><surname>Leung</surname><given-names>Ming-Ying</given-names></name><aff id="A4">Department of Mathematical Sciences, University of Texas at El Paso, El Paso, Texas 79968, USA</aff><email>mleung@utep.edu</email></contrib></contrib-group><pub-date pub-type="nihms-submitted"><day>14</day><month>5</month><year>2014</year></pub-date><pub-date pub-type="epub"><day>1</day><month>11</month><year>2004</year></pub-date><pub-date pub-type="ppub"><season>Fall</season><year>2004</year></pub-date><pub-date pub-type="pmc-release"><day>23</day><month>6</month><year>2014</year></pub-date><volume>16</volume><issue>4</issue><fpage>331</fpage><lpage>340</lpage><permissions><copyright-statement>©2004 INFORMS</copyright-statement><copyright-year>2004</copyright-year></permissions><abstract><p id="P1">With the identification of a novel coronavirus associated with the <italic>severe acute respiratory syndrome</italic> (SARS), computational analysis of its RNA genome sequence is expected to give useful clues to help elucidate the origin, evolution, and pathogenicity of the virus. In this paper, we study the collective counts of palindromes in the SARS genome along with all the completely sequenced coronaviruses. Based on a Markov-chain model for the genome sequence, the mean and standard deviation for the number of palindromes at or above a given length are derived. These theoretical results are complemented by extensive simulations to provide empirical estimates. Using a <italic>z</italic> score obtained from these mathematical and empirical means and standard deviations, we have observed that palindromes of length four are significantly underrepresented in all the coronaviruses in our data set. In contrast, length-six palindromes are significantly underrepresented only in the SARS coronavirus. Two other features are unique to the SARS sequence. First, there is a length-22 palindrome TCTTTAACAAGCTTGTTAAAGA spanning positions 25962–25983. Second, there are two repeating length-12 palindromes TTATAATTATAA spanning positions 22712–22723 and 22796–22807. Some further investigations into possible biological implications of these palindrome features are proposed.</p></abstract><kwd-group><kwd>Markov chain</kwd><kwd>palindrome counts</kwd><kwd>simulation</kwd><kwd>RNA viral genome</kwd><kwd>severe acute respiratory syndrome</kwd></kwd-group></article-meta></front></pmc><affiliations><list></list><tree><noCountry><name sortKey="Chew, David S H" sort="Chew, David S H" uniqKey="Chew D" first="David S. H." last="Chew">David S. H. Chew</name><name sortKey="Choi, Kwok Pui" sort="Choi, Kwok Pui" uniqKey="Choi K" first="Kwok Pui" last="Choi">Kwok Pui Choi</name><name sortKey="Heidner, Hans" sort="Heidner, Hans" uniqKey="Heidner H" first="Hans" last="Heidner">Hans Heidner</name><name sortKey="Leung, Ming Ying" sort="Leung, Ming Ying" uniqKey="Leung M" first="Ming-Ying" last="Leung">Ming-Ying Leung</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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