Informational laws of genome structures
Identifieur interne : 001202 ( Main/Merge ); précédent : 001201; suivant : 001203Informational laws of genome structures
Auteurs : Vincenzo Bonnici [Italie] ; Vincenzo Manca [Italie]Source :
- Scientific Reports [ 2045-2322 ] ; 2016.
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Abstract
In recent years, the analysis of genomes by means of strings of length
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DOI: 10.1038/srep28840
PubMed: 27354155
PubMed Central: 4937431
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type="wicri:Area/Ncbi/Checkpoint">001678</idno><idno type="wicri:Area/Main/Merge">001202</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Informational laws of genome structures</title><author><name sortKey="Bonnici, Vincenzo" sort="Bonnici, Vincenzo" uniqKey="Bonnici V" first="Vincenzo" last="Bonnici">Vincenzo Bonnici</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>University of Verona, Department of Computer Science, University of Verona</institution>, Verona 37134,<country>Italy</country></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Center for BioMedical Computing, University of Verona</institution>, Verona, 37134,<country>Italy</country></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Manca, Vincenzo" sort="Manca, Vincenzo" uniqKey="Manca V" first="Vincenzo" last="Manca">Vincenzo Manca</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>University of Verona, Department of Computer Science, University of Verona</institution>, Verona 37134,<country>Italy</country></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Center for BioMedical Computing, University of Verona</institution>, Verona, 37134,<country>Italy</country></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Scientific Reports</title><idno type="eISSN">2045-2322</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Animals</term><term>Computational Biology</term><term>Entropy</term><term>Evolution, Molecular</term><term>Genome</term><term>Humans</term><term>Models, Genetic</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Animaux</term><term>Biologie informatique</term><term>Entropie</term><term>Génome</term><term>Humains</term><term>Modèles génétiques</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Animals</term><term>Computational Biology</term><term>Entropy</term><term>Evolution, Molecular</term><term>Genome</term><term>Humans</term><term>Models, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Animaux</term><term>Biologie informatique</term><term>Entropie</term><term>Génome</term><term>Humains</term><term>Modèles génétiques</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>In recent years, the analysis of genomes by means of strings of length <italic>k</italic> occurring in the genomes, called <italic>k</italic>-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value of <italic>k</italic> for applying information theoretic concepts that express intrinsic aspects of genomes. The value <italic>k</italic> = lg<sub>2</sub>(<italic>n</italic>), where <italic>n</italic> is the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balances <italic>entropic</italic> and <italic>anti-entropic</italic> components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Conrad, M" uniqKey="Conrad M">M. Conrad</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Conrad, M" uniqKey="Conrad M">M. Conrad</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Holland, J" uniqKey="Holland J">J. Holland</name></author><author><name sortKey="Mallot, H" uniqKey="Mallot H">H. Mallot</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cercignani, C" uniqKey="Cercignani C">C. Cercignani</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shannon, C E" uniqKey="Shannon C">C. E. Shannon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pincus, S M" uniqKey="Pincus S">S. M. 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