Genomic DNA k-mer spectra: models and modalities
Identifieur interne : 001376 ( Pmc/Checkpoint ); précédent : 001375; suivant : 001377Genomic DNA k-mer spectra: models and modalities
Auteurs : Benny Chor [Israël] ; David Horn [Israël] ; Nick Goldman [Royaume-Uni] ; Yaron Levy [Israël] ; Tim Massingham [Royaume-Uni]Source :
- Genome Biology [ 1465-6906 ] ; 2009.
Abstract
Tetrapods, unlike other organisms, have multimodal spectra of k-mers in their genomes
Url:
DOI: 10.1186/gb-2009-10-10-r108
PubMed: 19814784
PubMed Central: 2784323
Affiliations:
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Astronomy, Tel Aviv University, Klausner St, Ramat-Aviv, Tel-Aviv 39040</wicri:regionArea><wicri:noRegion>Tel-Aviv 39040</wicri:noRegion></affiliation></author><author><name sortKey="Goldman, Nick" sort="Goldman, Nick" uniqKey="Goldman N" first="Nick" last="Goldman">Nick Goldman</name><affiliation wicri:level="1"><nlm:aff id="I3">European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD</wicri:regionArea><wicri:noRegion>CB10 1SD</wicri:noRegion></affiliation></author><author><name sortKey="Levy, Yaron" sort="Levy, Yaron" uniqKey="Levy Y" first="Yaron" last="Levy">Yaron Levy</name><affiliation wicri:level="1"><nlm:aff id="I1">School of Computer Science, Tel Aviv University, Klausner St, Ramat-Aviv, Tel-Aviv 39040, Israel</nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea>School of Computer Science, Tel Aviv University, Klausner 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39040</wicri:noRegion></affiliation></author><author><name sortKey="Horn, David" sort="Horn, David" uniqKey="Horn D" first="David" last="Horn">David Horn</name><affiliation wicri:level="1"><nlm:aff id="I2">School of Physics and Astronomy, Tel Aviv University, Klausner St, Ramat-Aviv, Tel-Aviv 39040, Israel</nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea>School of Physics and Astronomy, Tel Aviv University, Klausner St, Ramat-Aviv, Tel-Aviv 39040</wicri:regionArea><wicri:noRegion>Tel-Aviv 39040</wicri:noRegion></affiliation></author><author><name sortKey="Goldman, Nick" sort="Goldman, Nick" uniqKey="Goldman N" first="Nick" last="Goldman">Nick Goldman</name><affiliation wicri:level="1"><nlm:aff id="I3">European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD</wicri:regionArea><wicri:noRegion>CB10 1SD</wicri:noRegion></affiliation></author><author><name sortKey="Levy, Yaron" sort="Levy, Yaron" uniqKey="Levy Y" first="Yaron" last="Levy">Yaron Levy</name><affiliation wicri:level="1"><nlm:aff id="I1">School of Computer Science, Tel Aviv University, Klausner St, Ramat-Aviv, Tel-Aviv 39040, Israel</nlm:aff><country xml:lang="fr">Israël</country><wicri:regionArea>School of Computer Science, Tel Aviv University, Klausner St, Ramat-Aviv, Tel-Aviv 39040</wicri:regionArea><wicri:noRegion>Tel-Aviv 39040</wicri:noRegion></affiliation></author><author><name sortKey="Massingham, Tim" sort="Massingham, Tim" uniqKey="Massingham T" first="Tim" last="Massingham">Tim Massingham</name><affiliation wicri:level="1"><nlm:aff id="I3">European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD</wicri:regionArea><wicri:noRegion>CB10 1SD</wicri:noRegion></affiliation></author></analytic><series><title level="j">Genome Biology</title><idno type="ISSN">1465-6906</idno><idno type="eISSN">1465-6914</idno><imprint><date when="2009">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Tetrapods, unlike other organisms, have multimodal spectra of k-mers in their genomes</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Robin, S" uniqKey="Robin S">S Robin</name></author><author><name sortKey="Schbath, S" uniqKey="Schbath S">S Schbath</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Reinert, G" uniqKey="Reinert G">G Reinert</name></author><author><name sortKey="Schbath, S" uniqKey="Schbath S">S Schbath</name></author><author><name sortKey="Waterman, Ms" uniqKey="Waterman M">MS Waterman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Otaki, Jm" uniqKey="Otaki J">JM Otaki</name></author><author><name sortKey="Ienaka, S" uniqKey="Ienaka S">S Ienaka</name></author><author><name sortKey="Gotoh, T" uniqKey="Gotoh T">T Gotoh</name></author><author><name sortKey="Yamamoto, H" uniqKey="Yamamoto H">H Yamamoto</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tuller, T" uniqKey="Tuller T">T Tuller</name></author><author><name sortKey="Chor, B" uniqKey="Chor B">B Chor</name></author><author><name sortKey="Nelson, N" uniqKey="Nelson N">N Nelson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="El Antri, S" uniqKey="El Antri S">S el antri</name></author><author><name sortKey="Bittoun, P" uniqKey="Bittoun P">P Bittoun</name></author><author><name sortKey="Mauffret, O" uniqKey="Mauffret O">O Mauffret</name></author><author><name sortKey="Monnot, M" uniqKey="Monnot M">M 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Genome Biol</journal-id><journal-title-group><journal-title>Genome Biology</journal-title></journal-title-group><issn pub-type="ppub">1465-6906</issn><issn pub-type="epub">1465-6914</issn><publisher><publisher-name>BioMed Central</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">19814784</article-id><article-id pub-id-type="pmc">2784323</article-id><article-id pub-id-type="publisher-id">gb-2009-10-10-r108</article-id><article-id pub-id-type="doi">10.1186/gb-2009-10-10-r108</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research</subject></subj-group></article-categories><title-group><article-title>Genomic DNA <italic>k</italic>-mer spectra: models and modalities</article-title></title-group><contrib-group><contrib contrib-type="author" corresp="yes" id="A1"><name><surname>Chor</surname><given-names>Benny</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>benny@cs.tau.ac.il</email></contrib><contrib contrib-type="author" id="A2"><name><surname>Horn</surname><given-names>David</given-names></name><xref ref-type="aff" rid="I2">2</xref><email>horn@tau.ac.il</email></contrib><contrib contrib-type="author" id="A3"><name><surname>Goldman</surname><given-names>Nick</given-names></name><xref ref-type="aff" rid="I3">3</xref><email>goldman@ebi.ac.uk</email></contrib><contrib contrib-type="author" id="A4"><name><surname>Levy</surname><given-names>Yaron</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>yaron@emza-vs.com</email></contrib><contrib contrib-type="author" id="A5"><name><surname>Massingham</surname><given-names>Tim</given-names></name><xref ref-type="aff" rid="I3">3</xref><email>tim.massingham@ebi.ac.uk</email></contrib></contrib-group><aff id="I1"><label>1</label>School of Computer Science, Tel Aviv University, Klausner St, Ramat-Aviv, Tel-Aviv 39040, Israel</aff><aff id="I2"><label>2</label>School of Physics and Astronomy, Tel Aviv University, Klausner St, Ramat-Aviv, Tel-Aviv 39040, Israel</aff><aff id="I3"><label>3</label>European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK</aff><pub-date pub-type="ppub"><year>2009</year></pub-date><pub-date pub-type="epub"><day>8</day><month>10</month><year>2009</year></pub-date><volume>10</volume><issue>10</issue><fpage>R108</fpage><lpage>R108</lpage><history><date date-type="received"><day>17</day><month>3</month><year>2009</year></date><date date-type="rev-recd"><day>14</day><month>8</month><year>2009</year></date><date date-type="accepted"><day>8</day><month>10</month><year>2009</year></date></history><permissions><copyright-statement>Copyright ©2009 Chor et al.; licensee BioMed Central Ltd.</copyright-statement><copyright-year>2009</copyright-year><copyright-holder>Chor et al.; licensee BioMed Central Ltd.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an open access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><self-uri xlink:href="http://genomebiology.com/2009/10/10/R108"></self-uri><abstract abstract-type="short"><p>Tetrapods, unlike other organisms, have multimodal spectra of k-mers in their genomes</p></abstract><abstract><sec><title>Background</title><p>The empirical frequencies of DNA <italic>k</italic>-mers in whole genome sequences provide an interesting perspective on genomic complexity, and the availability of large segments of genomic sequence from many organisms means that analysis of <italic>k</italic>-mers with non-trivial lengths is now possible.</p></sec><sec><title>Results</title><p>We have studied the <italic>k</italic>-mer spectra of more than 100 species from Archea, Bacteria, and Eukaryota, particularly looking at the modalities of the distributions. As expected, most species have a unimodal <italic>k</italic>-mer spectrum. However, a few species, including all mammals, have multimodal spectra. These species coincide with the tetrapods. Genomic sequences are clearly very complex, and cannot be fully explained by any simple probabilistic model. Yet we sought such an explanation for the observed modalities, and discovered that low-order Markov models capture this property (and some others) fairly well.</p></sec><sec><title>Conclusions</title><p>Multimodal spectra are characterized by specific ranges of values of C+G content and of CpG dinucleotide suppression, a range that encompasses all tetrapods analyzed. Other genomes, like that of the protozoa <italic>Entamoeba histolytica</italic>, which also exhibits CpG suppression, do not have multimodal <italic>k</italic>-mer spectra. Groupings of functional elements of the human genome also have a clear modality, and exhibit either a unimodal or multimodal behaviour, depending on the two above mentioned values.</p></sec></abstract></article-meta></front></pmc><affiliations><list><country><li>Israël</li><li>Royaume-Uni</li></country></list><tree><country name="Israël"><noRegion><name sortKey="Chor, Benny" sort="Chor, Benny" uniqKey="Chor B" first="Benny" last="Chor">Benny Chor</name></noRegion><name sortKey="Horn, David" sort="Horn, David" uniqKey="Horn D" first="David" last="Horn">David Horn</name><name sortKey="Levy, Yaron" sort="Levy, Yaron" uniqKey="Levy Y" first="Yaron" last="Levy">Yaron Levy</name></country><country name="Royaume-Uni"><noRegion><name sortKey="Goldman, Nick" sort="Goldman, Nick" uniqKey="Goldman N" first="Nick" last="Goldman">Nick Goldman</name></noRegion><name sortKey="Massingham, Tim" sort="Massingham, Tim" uniqKey="Massingham T" first="Tim" last="Massingham">Tim Massingham</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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