Is a Genome a Codeword of an Error-Correcting Code?
Identifieur interne : 000518 ( Pmc/Curation ); précédent : 000517; suivant : 000519Is a Genome a Codeword of an Error-Correcting Code?
Auteurs : Luzinete C. B. Faria [Brésil] ; Andréa S. L. Rocha [Brésil] ; João H. Kleinschmidt [Brésil] ; Márcio C. Silva-Filho [Brésil] ; Edson Bim [Brésil] ; Roberto H. Herai [États-Unis] ; Michel E. B. Yamagishi [Brésil] ; Reginaldo Palazzo [Brésil]Source :
- PLoS ONE [ 1932-6203 ] ; 2012.
Abstract
Since a genome is a discrete sequence, the elements of which belong to a set of four letters, the question as to whether or not there is an error-correcting code underlying DNA sequences is unavoidable. The most common approach to answering this question is to propose a methodology to verify the existence of such a code. However, none of the methodologies proposed so far, although quite clever, has achieved that goal. In a recent work, we showed that DNA sequences can be identified as codewords in a class of cyclic error-correcting codes known as Hamming codes. In this paper, we show that a complete intron-exon gene, and even a plasmid genome, can be identified as a Hamming code codeword as well. Although this does not constitute a definitive proof that there is an error-correcting code underlying DNA sequences, it is the first evidence in this direction.
Url:
DOI: 10.1371/journal.pone.0036644
PubMed: 22649495
PubMed Central: 3359345
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B." last="Faria">Luzinete C. B. Faria</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Departamento de Telemática, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil</addr-line></nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Telemática, Universidade Estadual de Campinas, Campinas, São Paulo</wicri:regionArea></affiliation></author><author><name sortKey="Rocha, Andrea S L" sort="Rocha, Andrea S L" uniqKey="Rocha A" first="Andréa S. L." last="Rocha">Andréa S. L. Rocha</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Departamento de Telemática, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil</addr-line></nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Telemática, Universidade Estadual de Campinas, Campinas, São Paulo</wicri:regionArea></affiliation></author><author><name sortKey="Kleinschmidt, Joao H" sort="Kleinschmidt, Joao H" uniqKey="Kleinschmidt J" first="João H." last="Kleinschmidt">João H. Kleinschmidt</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Centro de Engenharia, Modelagem e Ciências Sociais Aplicadas, Universidade Federal do ABC, Santo André, São Paulo, Brazil</addr-line></nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Centro de Engenharia, Modelagem e Ciências Sociais Aplicadas, Universidade Federal do ABC, Santo André, São Paulo</wicri:regionArea></affiliation></author><author><name sortKey="Silva Filho, Marcio C" sort="Silva Filho, Marcio C" uniqKey="Silva Filho M" first="Márcio C." last="Silva-Filho">Márcio C. Silva-Filho</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, São Paulo, Brazil</addr-line></nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, São Paulo</wicri:regionArea></affiliation></author><author><name sortKey="Bim, Edson" sort="Bim, Edson" uniqKey="Bim E" first="Edson" last="Bim">Edson Bim</name><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>Departamento de Sistema de Controle de Energia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil</addr-line></nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Sistema de Controle de Energia, Universidade Estadual de Campinas, Campinas, São Paulo</wicri:regionArea></affiliation></author><author><name sortKey="Herai, Roberto H" sort="Herai, Roberto H" uniqKey="Herai R" first="Roberto H." last="Herai">Roberto H. Herai</name><affiliation wicri:level="1"><nlm:aff id="aff5"><addr-line>Department of Cellular & Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Cellular & Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, California</wicri:regionArea></affiliation></author><author><name sortKey="Yamagishi, Michel E B" sort="Yamagishi, Michel E B" uniqKey="Yamagishi M" first="Michel E. B." last="Yamagishi">Michel E. B. Yamagishi</name><affiliation wicri:level="1"><nlm:aff id="aff6"><addr-line>Embrapa Informática Agropecuária, Laboratório de Bioinformática Aplicada, Campinas, São Paulo, Brazil</addr-line></nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Embrapa Informática Agropecuária, Laboratório de Bioinformática Aplicada, Campinas, São Paulo</wicri:regionArea></affiliation></author><author><name sortKey="Palazzo, Reginaldo" sort="Palazzo, Reginaldo" uniqKey="Palazzo R" first="Reginaldo" last="Palazzo">Reginaldo Palazzo</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Departamento de Telemática, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil</addr-line></nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea>Departamento de Telemática, Universidade Estadual de Campinas, Campinas, São Paulo</wicri:regionArea></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Since a genome is a discrete sequence, the elements of which belong to a set of four letters, the question as to whether or not there is an error-correcting code underlying DNA sequences is unavoidable. The most common approach to answering this question is to propose a methodology to verify the existence of such a code. However, none of the methodologies proposed so far, although quite clever, has achieved that goal. In a recent work, we showed that DNA sequences can be identified as codewords in a class of cyclic error-correcting codes known as Hamming codes. In this paper, we show that a complete intron-exon gene, and even a plasmid genome, can be identified as a Hamming code codeword as well. Although this does not constitute a definitive proof that there is an error-correcting code underlying DNA sequences, it is the first evidence in this direction.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Schneider, Td" uniqKey="Schneider T">TD Schneider</name></author><author><name sortKey="Stormo, Gd" uniqKey="Stormo G">GD Stormo</name></author><author><name sortKey="Gold, L" uniqKey="Gold L">L Gold</name></author><author><name sortKey="Ehrenfeucht, A" uniqKey="Ehrenfeucht A">A Ehrenfeucht</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kumar, Rp" uniqKey="Kumar R">RP Kumar</name></author><author><name sortKey="Senthikumar, R" uniqKey="Senthikumar R">R Senthikumar</name></author><author><name sortKey="Singh, V" uniqKey="Singh V">V Singh</name></author><author><name sortKey="Mishra, Rk" uniqKey="Mishra R">RK Mishra</name></author></analytic></biblStruct><biblStruct><analytic><author><name 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Faria</name></author><author><name sortKey="Rocha, Asl" uniqKey="Rocha A">ASL Rocha</name></author><author><name sortKey="Kleinschmidt, Jh" uniqKey="Kleinschmidt J">JH Kleinschmidt</name></author><author><name sortKey="Palazzo, R" uniqKey="Palazzo R">R Palazzo</name></author><author><name sortKey="Silva Filho, Mc" uniqKey="Silva Filho M">MC Silva-Filho</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hocquenghem, A" uniqKey="Hocquenghem A">A Hocquenghem</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bose, Rc" uniqKey="Bose R">RC Bose</name></author><author><name sortKey="Chaudhuri, Dk" uniqKey="Chaudhuri D">DK Chaudhuri</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mcwilliams, Fj" uniqKey="Mcwilliams F">FJ McWilliams</name></author><author><name sortKey="Sloane, Nja" uniqKey="Sloane N">NJA Sloane</name></author></analytic></biblStruct><biblStruct><analytic><author><name 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uniqKey="Palazzo R">R Palazzo</name></author><author><name sortKey="Silva Filho, Mc" uniqKey="Silva Filho M">MC Silva-Filho</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">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">22649495</article-id><article-id pub-id-type="pmc">3359345</article-id><article-id pub-id-type="publisher-id">PONE-D-11-25045</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0036644</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Biology</subject><subj-group><subject>Computational Biology</subject><subj-group><subject>Genomics</subject><subj-group><subject>Genome Analysis Tools</subject></subj-group></subj-group><subj-group><subject>Molecular Genetics</subject><subj-group><subject>Gene Identification and Analysis</subject></subj-group></subj-group><subj-group><subject>Sequence Analysis</subject></subj-group></subj-group><subj-group><subject>Genetics</subject></subj-group></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Computer Science</subject><subj-group><subject>Algorithms</subject></subj-group><subj-group><subject>Computer Modeling</subject></subj-group></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Engineering</subject></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Mathematics</subject><subj-group><subject>Applied Mathematics</subject></subj-group><subj-group><subject>Mathematical Computing</subject></subj-group></subj-group></article-categories><title-group><article-title>Is a Genome a Codeword of an Error-Correcting Code?</article-title><alt-title alt-title-type="running-head">Is a Genome a Codeword of an ECC?</alt-title></title-group><contrib-group><contrib contrib-type="author" equal-contrib="yes"><name><surname>Faria</surname><given-names>Luzinete C. B.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib><contrib contrib-type="author" equal-contrib="yes"><name><surname>Rocha</surname><given-names>Andréa S. L.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Kleinschmidt</surname><given-names>João H.</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Silva-Filho</surname><given-names>Márcio C.</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Bim</surname><given-names>Edson</given-names></name><xref ref-type="aff" rid="aff4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Herai</surname><given-names>Roberto H.</given-names></name><xref ref-type="aff" rid="aff5"><sup>5</sup></xref></contrib><contrib contrib-type="author"><name><surname>Yamagishi</surname><given-names>Michel E. B.</given-names></name><xref ref-type="aff" rid="aff6"><sup>6</sup></xref></contrib><contrib contrib-type="author"><name><surname>Palazzo</surname><given-names>Reginaldo</given-names><suffix>Jr</suffix></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib></contrib-group><aff id="aff1"><label>1</label><addr-line>Departamento de Telemática, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil</addr-line></aff><aff id="aff2"><label>2</label><addr-line>Centro de Engenharia, Modelagem e Ciências Sociais Aplicadas, Universidade Federal do ABC, Santo André, São Paulo, Brazil</addr-line></aff><aff id="aff3"><label>3</label><addr-line>Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, São Paulo, Brazil</addr-line></aff><aff id="aff4"><label>4</label><addr-line>Departamento de Sistema de Controle de Energia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil</addr-line></aff><aff id="aff5"><label>5</label><addr-line>Department of Cellular & Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, California, United States of America</addr-line></aff><aff id="aff6"><label>6</label><addr-line>Embrapa Informática Agropecuária, Laboratório de Bioinformática Aplicada, Campinas, São Paulo, Brazil</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Wu</surname><given-names>Rongling</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1">Pennsylvania State University, United States of America</aff><author-notes><corresp id="cor1">* E-mail: <email>luzinete@dt.fee.unicamp.br</email> (LCBF); <email>andrea@dt.fee.unicamp.br</email> (ASLR)</corresp><fn fn-type="con"><p>Conceived and designed the experiments: LCBF ASLR RP. Performed the experiments: LCBF ASLR. Analyzed the data: LCBF ASLR JHK MCSF EB RH MY RP. Wrote the paper: LCBF ASLR JHK MCSF EB RH MY RP. Developed the software: JHK. Conceived and designed the study: RP.</p></fn></author-notes><pub-date pub-type="collection"><year>2012</year></pub-date><pub-date pub-type="epub"><day>23</day><month>5</month><year>2012</year></pub-date><volume>7</volume><issue>5</issue><elocation-id>e36644</elocation-id><history><date date-type="received"><day>14</day><month>12</month><year>2011</year></date><date date-type="accepted"><day>4</day><month>4</month><year>2012</year></date></history><permissions><copyright-statement>Faria et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</copyright-statement><copyright-year>2012</copyright-year></permissions><abstract><p>Since a genome is a discrete sequence, the elements of which belong to a set of four letters, the question as to whether or not there is an error-correcting code underlying DNA sequences is unavoidable. The most common approach to answering this question is to propose a methodology to verify the existence of such a code. However, none of the methodologies proposed so far, although quite clever, has achieved that goal. In a recent work, we showed that DNA sequences can be identified as codewords in a class of cyclic error-correcting codes known as Hamming codes. In this paper, we show that a complete intron-exon gene, and even a plasmid genome, can be identified as a Hamming code codeword as well. Although this does not constitute a definitive proof that there is an error-correcting code underlying DNA sequences, it is the first evidence in this direction.</p></abstract><counts><page-count count="9"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Curation/RBID.i -Sk "pubmed:22649495" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Curation/biblio.hfd \
| NlmPubMed2Wicri -a TelematiV1
| This area was generated with Dilib version V0.6.31. |  |