MersV1, PubMed, Corpus, bibRecord, 001068

Informational laws of genome structures.

Identifieur interne : 001068 ( PubMed/Corpus ); précédent : 001067; suivant : 001069

Informational laws of genome structures.

Auteurs : Vincenzo Bonnici ; Vincenzo Manca

Source :

Scientific reports [ 2045-2322 ] ; 2016.

RBID : pubmed:27354155

English descriptors

KwdEn :
- Algorithms, Animals, Computational Biology, Entropy, Evolution, Molecular, Genome, Humans, Models, Genetic.
MESH :
- Algorithms, Animals, Computational Biology, Entropy, Evolution, Molecular, Genome, Humans, Models, Genetic.

Abstract

In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-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 k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n 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 entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined.

DOI: 10.1038/srep28840
PubMed: 27354155

Links to Exploration step

pubmed:27354155

Le document en format XML

<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">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><nlm:affiliation>University of Verona, Department of Computer Science, University of Verona, Verona 37134, Italy.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Manca, Vincenzo" sort="Manca, Vincenzo" uniqKey="Manca V" first="Vincenzo" last="Manca">Vincenzo Manca</name>
<affiliation><nlm:affiliation>University of Verona, Department of Computer Science, University of Verona, Verona 37134, Italy.</nlm:affiliation>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2016">2016</date>
<idno type="RBID">pubmed:27354155</idno>
<idno type="pmid">27354155</idno>
<idno type="doi">10.1038/srep28840</idno>
<idno type="wicri:Area/PubMed/Corpus">001068</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001068</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">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><nlm:affiliation>University of Verona, Department of Computer Science, University of Verona, Verona 37134, Italy.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Manca, Vincenzo" sort="Manca, Vincenzo" uniqKey="Manca V" first="Vincenzo" last="Manca">Vincenzo Manca</name>
<affiliation><nlm:affiliation>University of Verona, Department of Computer Science, University of Verona, Verona 37134, Italy.</nlm:affiliation>
</affiliation>
</author>
</analytic>
<series><title level="j">Scientific reports</title>
<idno type="eISSN">2045-2322</idno>
<imprint><date when="2016" type="published">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="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>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-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 k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n 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 entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined.</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">27354155</PMID>
<DateCompleted><Year>2018</Year>
<Month>05</Month>
<Day>30</Day>
</DateCompleted>
<DateRevised><Year>2018</Year>
<Month>11</Month>
<Day>13</Day>
</DateRevised>
<Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2045-2322</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>6</Volume>
<PubDate><Year>2016</Year>
<Month>06</Month>
<Day>29</Day>
</PubDate>
</JournalIssue>
<Title>Scientific reports</Title>
<ISOAbbreviation>Sci Rep</ISOAbbreviation>
</Journal>
<ArticleTitle>Informational laws of genome structures.</ArticleTitle>
<Pagination><MedlinePgn>28840</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1038/srep28840</ELocationID>
<Abstract><AbstractText>In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-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 k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n 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 entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Bonnici</LastName>
<ForeName>Vincenzo</ForeName>
<Initials>V</Initials>
<AffiliationInfo><Affiliation>University of Verona, Department of Computer Science, University of Verona, Verona 37134, Italy.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Center for BioMedical Computing, University of Verona, Verona, 37134, Italy.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Manca</LastName>
<ForeName>Vincenzo</ForeName>
<Initials>V</Initials>
<AffiliationInfo><Affiliation>University of Verona, Department of Computer Science, University of Verona, Verona 37134, Italy.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Center for BioMedical Computing, University of Verona, Verona, 37134, Italy.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic"><Year>2016</Year>
<Month>06</Month>
<Day>29</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>England</Country>
<MedlineTA>Sci Rep</MedlineTA>
<NlmUniqueID>101563288</NlmUniqueID>
<ISSNLinking>2045-2322</ISSNLinking>
</MedlineJournalInfo>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList><MeshHeading><DescriptorName UI="D000465" MajorTopicYN="N">Algorithms</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D019277" MajorTopicYN="N">Entropy</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D016678" MajorTopicYN="Y">Genome</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D008957" MajorTopicYN="Y">Models, Genetic</DescriptorName>
</MeshHeading>
</MeshHeadingList>
</MedlineCitation>
<PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year>
<Month>02</Month>
<Day>01</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted"><Year>2016</Year>
<Month>06</Month>
<Day>09</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez"><Year>2016</Year>
<Month>6</Month>
<Day>30</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed"><Year>2016</Year>
<Month>6</Month>
<Day>30</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline"><Year>2018</Year>
<Month>5</Month>
<Day>31</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>epublish</PublicationStatus>
<ArticleIdList><ArticleId IdType="pubmed">27354155</ArticleId>
<ArticleId IdType="pii">srep28840</ArticleId>
<ArticleId IdType="doi">10.1038/srep28840</ArticleId>
<ArticleId IdType="pmc">PMC4937431</ArticleId>
</ArticleIdList>
<ReferenceList><Reference><Citation>Proc Natl Acad Sci U S A. 1991 Mar 15;88(6):2297-301</Citation>
<ArticleIdList><ArticleId IdType="pubmed">11607165</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Comput Chem. 1999 Jun 15;23(3-4):275-82</Citation>
<ArticleIdList><ArticleId IdType="pubmed">10404620</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Theor Biol. 1966 Feb;10(2):281-300</Citation>
<ArticleIdList><ArticleId IdType="pubmed">5964394</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Biol Direct. 2010 Oct 12;5:59</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20937149</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Science. 2016 Mar 25;351(6280):aad6253</Citation>
<ArticleIdList><ArticleId IdType="pubmed">27013737</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Proc Natl Acad Sci U S A. 1999 Aug 3;96(16):9184-9</Citation>
<ArticleIdList><ArticleId IdType="pubmed">10430917</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Comput Biol Chem. 2014 Dec;53 Pt A:1-4</Citation>
<ArticleIdList><ArticleId IdType="pubmed">25239778</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Bioinformatics. 2011 Apr 15;27(8):1061-7</Citation>
<ArticleIdList><ArticleId IdType="pubmed">21317142</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Jun;79(6 Pt 1):061911</Citation>
<ArticleIdList><ArticleId IdType="pubmed">19658528</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Theor Biol. 2015 Dec 21;387:88-100</Citation>
<ArticleIdList><ArticleId IdType="pubmed">26427337</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nucleic Acids Res. 2012 Jan;40(Database issue):D136-43</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22139910</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Science. 2003 Nov 21;302(5649):1401-4</Citation>
<ArticleIdList><ArticleId IdType="pubmed">14631042</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Math Biosci. 2008 Feb;211(2):282-98</Citation>
<ArticleIdList><ArticleId IdType="pubmed">17931667</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>BMC Genomics. 2008 Oct 31;9:517</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18976482</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Brief Bioinform. 2014 May;15(3):376-89</Citation>
<ArticleIdList><ArticleId IdType="pubmed">24058049</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>BMC Bioinformatics. 2007 Oct 16;8:393</Citation>
<ArticleIdList><ArticleId IdType="pubmed">17939871</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Oct;64(4 Pt 1):041917</Citation>
<ArticleIdList><ArticleId IdType="pubmed">11690062</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Bioinformatics. 2004 Oct 12;20(15):2421-8</Citation>
<ArticleIdList><ArticleId IdType="pubmed">15087315</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Biol Direct. 2015 Sep 16;10:53</Citation>
<ArticleIdList><ArticleId IdType="pubmed">26376976</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>BMC Genomics. 2012 Sep 17;13:485</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22985068</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Gene. 2014 Aug 1;546(1):25-34</Citation>
<ArticleIdList><ArticleId IdType="pubmed">24858075</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Bull Math Biol. 1987;49(6):737-59</Citation>
<ArticleIdList><ArticleId IdType="pubmed">2832024</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Genome Biol. 2009;10(10):R108</Citation>
<ArticleIdList><ArticleId IdType="pubmed">19814784</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Theor Biol. 2000 Oct 7;206(3):379-86</Citation>
<ArticleIdList><ArticleId IdType="pubmed">10988023</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
</PubmedData>
</pubmed>
</record>

Pour manipuler ce document sous Unix (Dilib)

EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/PubMed/Corpus

HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001068 | SxmlIndent | more

HfdSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd -nk 001068 | SxmlIndent | more

Pour mettre un lien sur cette page dans le réseau Wicri

{{Explor lien
   |wiki=    Sante
   |area=    MersV1
   |flux=    PubMed
   |étape=   Corpus
   |type=    RBID
   |clé=     pubmed:27354155
   |texte=   Informational laws of genome structures.
}}

Pour générer des pages wiki

HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/RBID.i   -Sk "pubmed:27354155" \
       | HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd   \
       | NlmPubMed2Wicri -a MersV1

This area was generated with Dilib version V0.6.33.
Data generation: Mon Apr 20 23:26:43 2020. Site generation: Sat Mar 27 09:06:09 2021

	Serveur d'exploration MERS
	Attention, ce site est en cours de développement ! Attention, site généré par des moyens informatiques à partir de corpus bruts. Les informations ne sont donc pas validées.

Serveur d'exploration MERS

Informational laws of genome structures.

Informational laws of genome structures.

Source :

English descriptors

Abstract

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki