Comparative Analysis of DNA Word Abundances in Four Yeast Genomes Using a Novel Statistical Background Model
Identifieur interne : 002034 ( Main/Exploration ); précédent : 002033; suivant : 002035Comparative Analysis of DNA Word Abundances in Four Yeast Genomes Using a Novel Statistical Background Model
Auteurs : Ramkumar Hariharan [Inde, Japon] ; Reji Simon [Inde] ; M. Radhakrishna Pillai [Inde] ; Todd D. Taylor [Japon]Source :
- PLoS ONE [ 1932-6203 ] ; 2013.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , analysis : DNA, Fungal.
- genetics : Saccharomyces.
- methods : Genomics.
- Algorithms, Binding Sites, DNA, Intergenic, Genome, Fungal, Markov Chains, Models, Genetic, Models, Statistical, Open Reading Frames, Sequence Analysis, DNA, Species Specificity.
Abstract
Previous studies have shown that the identification and analysis of both abundant and rare k-mers or “DNA words of length k” in genomic sequences using suitable statistical background models can reveal biologically significant sequence elements. Other studies have investigated the uni/multimodal distribution of k-mer abundances or “k-mer spectra” in different DNA sequences. However, the existing background models are affected to varying extents by compositional bias. Moreover, the distribution of k-mer abundances in the context of related genomes has not been studied previously. Here, we present a novel statistical background model for calculating k-mer enrichment in DNA sequences based on the average of the frequencies of the two (k-1) mers for each k-mer. Comparison of our null model with the commonly used ones, including Markov models of different orders and the single mismatch model, shows that our method is more robust to compositional AT-rich bias and detects many additional, repeat-poor over-abundant k-mers that are biologically meaningful. Analysis of overrepresented genomic k-mers (4≤k≤16) from four yeast species using this model showed that the fraction of overrepresented DNA words falls linearly as k increases; however, a significant number of overabundant k-mers exists at higher values of k. Finally, comparative analysis of k-mer abundance scores across four yeast species revealed a mixture of unimodal and multimodal spectra for the various genomic sub-regions analyzed.
Url:
DOI: 10.1371/journal.pone.0058038
PubMed: 23472131
PubMed Central: 3589456
Affiliations:
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Radhakrishna" last="Pillai">M. Radhakrishna Pillai</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Cancer Research Program, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Cancer Research Program, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala</wicri:regionArea><wicri:noRegion>Kerala</wicri:noRegion></affiliation></author><author><name sortKey="Taylor, Todd D" sort="Taylor, Todd D" uniqKey="Taylor T" first="Todd D." last="Taylor">Todd D. Taylor</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Laboratory for MetaSystems Research, RIKEN Quantitative Biology Center, Tsurumi-ku, Yokohama, Kanagawa, Japan</addr-line></nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Laboratory for MetaSystems Research, RIKEN Quantitative Biology Center, Tsurumi-ku, Yokohama, Kanagawa</wicri:regionArea><wicri:noRegion>Kanagawa</wicri:noRegion></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Binding Sites</term><term>DNA, Fungal (analysis)</term><term>DNA, Intergenic</term><term>Genome, Fungal</term><term>Genomics (methods)</term><term>Markov Chains</term><term>Models, Genetic</term><term>Models, Statistical</term><term>Open Reading Frames</term><term>Saccharomyces (genetics)</term><term>Sequence Analysis, DNA</term><term>Species Specificity</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN fongique (analyse)</term><term>ADN intergénique</term><term>Algorithmes</term><term>Analyse de séquence d'ADN</term><term>Cadres ouverts de lecture</term><term>Chaines de Markov</term><term>Génome fongique</term><term>Génomique ()</term><term>Modèles génétiques</term><term>Modèles statistiques</term><term>Saccharomyces (génétique)</term><term>Sites de fixation</term><term>Spécificité d'espèce</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>DNA, Fungal</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>ADN fongique</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Saccharomyces</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Saccharomyces</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Binding Sites</term><term>DNA, Intergenic</term><term>Genome, Fungal</term><term>Markov Chains</term><term>Models, Genetic</term><term>Models, Statistical</term><term>Open Reading Frames</term><term>Sequence Analysis, DNA</term><term>Species Specificity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN intergénique</term><term>Algorithmes</term><term>Analyse de séquence d'ADN</term><term>Cadres ouverts de lecture</term><term>Chaines de Markov</term><term>Génome fongique</term><term>Génomique</term><term>Modèles génétiques</term><term>Modèles statistiques</term><term>Sites de fixation</term><term>Spécificité d'espèce</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Previous studies have shown that the identification and analysis of both abundant and rare k-mers or “DNA words of length k” in genomic sequences using suitable statistical background models can reveal biologically significant sequence elements. Other studies have investigated the uni/multimodal distribution of k-mer abundances or “k-mer spectra” in different DNA sequences. However, the existing background models are affected to varying extents by compositional bias. Moreover, the distribution of k-mer abundances in the context of related genomes has not been studied previously. Here, we present a novel statistical background model for calculating k-mer enrichment in DNA sequences based on the average of the frequencies of the two (k-1) mers for each k-mer. Comparison of our null model with the commonly used ones, including Markov models of different orders and the single mismatch model, shows that our method is more robust to compositional AT-rich bias and detects many additional, repeat-poor over-abundant k-mers that are biologically meaningful. Analysis of overrepresented genomic k-mers (4≤k≤16) from four yeast species using this model showed that the fraction of overrepresented DNA words falls linearly as k increases; however, a significant number of overabundant k-mers exists at higher values of k. Finally, comparative analysis of k-mer abundance scores across four yeast species revealed a mixture of unimodal and multimodal spectra for the various genomic sub-regions analyzed.</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="Chor, B" uniqKey="Chor B">B Chor</name></author><author><name sortKey="Horn, D" uniqKey="Horn D">D Horn</name></author><author><name sortKey="Goldman, N" uniqKey="Goldman N">N Goldman</name></author><author><name 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Hampikian</name></author><author><name sortKey="Andersen, T" uniqKey="Andersen T">T Andersen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Garcia, Sp" uniqKey="Garcia S">SP Garcia</name></author><author><name sortKey="Pinho, Aj" uniqKey="Pinho A">AJ Pinho</name></author><author><name sortKey="Rodrigues, Jm" uniqKey="Rodrigues J">JM Rodrigues</name></author><author><name sortKey="Bastos, Ca" uniqKey="Bastos C">CA Bastos</name></author><author><name sortKey="Ferreira, Pj" uniqKey="Ferreira P">PJ Ferreira</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Herold, J" uniqKey="Herold J">J Herold</name></author><author><name sortKey="Kurtz, S" uniqKey="Kurtz S">S Kurtz</name></author><author><name sortKey="Giegerich, R" uniqKey="Giegerich R">R Giegerich</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brazma, A" uniqKey="Brazma A">A Brazma</name></author><author><name sortKey="Jonassen, 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Estep</name></author><author><name sortKey="Tavazoie, S" uniqKey="Tavazoie S">S Tavazoie</name></author><author><name sortKey="Church, Gm" uniqKey="Church G">GM Church</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Helden, J" uniqKey="Van Helden J">J van Helden</name></author><author><name sortKey="Andre, B" uniqKey="Andre B">B André</name></author><author><name sortKey="Collado Vides, J" uniqKey="Collado Vides J">J Collado-Vides</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sinha, S" uniqKey="Sinha S">S Sinha</name></author><author><name sortKey="Tompa, M" uniqKey="Tompa M">M Tompa</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Xie, X" uniqKey="Xie X">X Xie</name></author><author><name sortKey="Mikkelsen, Ts" uniqKey="Mikkelsen T">TS Mikkelsen</name></author><author><name sortKey="Gnirke, A" uniqKey="Gnirke A">A Gnirke</name></author><author><name sortKey="Lindblad Toh, K" uniqKey="Lindblad Toh K">K Lindblad-Toh</name></author><author><name sortKey="Kellis, M" uniqKey="Kellis M">M Kellis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hampson, S" uniqKey="Hampson S">S Hampson</name></author><author><name sortKey="Kibler, D" uniqKey="Kibler D">D Kibler</name></author><author><name sortKey="Baldi, P" uniqKey="Baldi P">P Baldi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pinho, Aj" uniqKey="Pinho A">AJ Pinho</name></author><author><name sortKey="Ferreira, Pj" uniqKey="Ferreira P">PJ Ferreira</name></author><author><name sortKey="Garcia, Sp" uniqKey="Garcia S">SP Garcia</name></author><author><name sortKey="Rodrigues, Jm" uniqKey="Rodrigues J">JM Rodrigues</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Abdulrehman, D" uniqKey="Abdulrehman D">D Abdulrehman</name></author><author><name sortKey="Monteiro, Pt" uniqKey="Monteiro P">PT Monteiro</name></author><author><name sortKey="Teixeira, Mc" uniqKey="Teixeira M">MC Teixeira</name></author><author><name sortKey="Mira, Np" uniqKey="Mira N">NP Mira</name></author><author><name sortKey="Lourenco, Ab" uniqKey="Lourenco A">AB Lourenço</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Burge, C" uniqKey="Burge C">C Burge</name></author><author><name sortKey="Campbell, Am" uniqKey="Campbell A">AM Campbell</name></author><author><name sortKey="Karlin, S" uniqKey="Karlin S">S Karlin</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Inde</li><li>Japon</li></country></list><tree><country name="Inde"><noRegion><name sortKey="Hariharan, Ramkumar" sort="Hariharan, Ramkumar" uniqKey="Hariharan R" first="Ramkumar" last="Hariharan">Ramkumar Hariharan</name></noRegion><name sortKey="Pillai, M Radhakrishna" sort="Pillai, M Radhakrishna" uniqKey="Pillai M" first="M. Radhakrishna" last="Pillai">M. Radhakrishna Pillai</name><name sortKey="Simon, Reji" sort="Simon, Reji" uniqKey="Simon R" first="Reji" last="Simon">Reji Simon</name></country><country name="Japon"><noRegion><name sortKey="Hariharan, Ramkumar" sort="Hariharan, Ramkumar" uniqKey="Hariharan R" first="Ramkumar" last="Hariharan">Ramkumar Hariharan</name></noRegion><name sortKey="Taylor, Todd D" sort="Taylor, Todd D" uniqKey="Taylor T" first="Todd D." last="Taylor">Todd D. Taylor</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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