Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/189
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dc.contributor.authorEskesen, STen
dc.contributor.authorEskesen, FNen
dc.contributor.authorKinghorn, Ben
dc.contributor.authorRuvinsky, Aen
dc.date.accessioned2008-05-06T16:17:00Z-
dc.date.issued2004-
dc.identifier.citationBMC Molecular Biology, 5(12), p. 1-11en
dc.identifier.issn1471-2199en
dc.identifier.urihttps://hdl.handle.net/1959.11/189-
dc.description.abstractBACKGROUND: The periodic pattern of DNA in exons is a known phenomenon. It was suggested that one of the initial causes of periodicity could be the universal (RNY)npattern (R = A or G, Y= C or U, N = any base) of ancient RNA. Two major questions were addressed in this paper.Firstly, the cause of DNA periodicity, which was investigated by comparisons between real and simulated coding sequences. Secondly, quantification of DNA periodicity was made using anevolutionary algorithm, which was not previously used for such purposes.RESULTS: We have shown that simulated coding sequences, which were composed using codon usage frequencies only, demonstrate DNA periodicity very similar to the observed in real exons.It was also found that DNA periodicity disappears in the simulated sequences, when the frequencies of codons become equal.Frequencies of the nucleotides (and the dinucleotide AG) at each location along phase 0 exons were calculated for C. elegans, D. melanogaster and H. sapiens. Two models were used to fit thesedata, with the key objective of describing periodicity. Both of the models showed that the best-fit curves closely matched the actual data points. The first dynamic period determination modelconsistently generated a value, which was very close to the period equal to 3 nucleotides. The second fixed period model, as expected, kept the period exactly equal to 3 and did not detract from its goodness of fit.CONCLUSIONS: Conclusion can be drawn that DNA periodicity in exons is determined by codon usage frequencies. It is essential to differentiate between DNA periodicity itself, and the length ofthe period equal to 3. Periodicity itself is a result of certain combinations of codons with different frequencies typical for a species. The length of period equal to 3, instead, is caused by the triplet nature of genetic code. The models and evolutionary algorithm used for characterising DNA periodicity are proven to be an effective tool for describing the periodicity pattern in a species, when a number of exons in the same phase are analysed.en
dc.languageenen
dc.publisherBioMed Central Ltden
dc.relation.ispartofBMC Molecular Biologyen
dc.titlePeriodicity of DNA in Exonsen
dc.typeJournal Articleen
dc.identifier.doi10.1186/1471-2199-5-12en
dcterms.accessRightsUNE Greenen
dc.subject.keywordsAnimal Breedingen
local.contributor.firstnameSTen
local.contributor.firstnameFNen
local.contributor.firstnameBen
local.contributor.firstnameAen
local.subject.for2008070201 Animal Breedingen
local.subject.seo630101 Sheep - meaten
local.profile.schoolSchool of Environmental and Rural Scienceen
local.profile.schoolSchool of Environmental and Rural Scienceen
local.profile.schoolSchool of Environmental and Rural Scienceen
local.profile.emailseskesen@une.edu.auen
local.profile.emailbkinghor@une.edu.auen
local.profile.emailaruvinsk@une.edu.auen
local.output.categoryC1en
local.record.placeauen
local.record.institutionUniversity of New Englanden
local.identifier.epublicationsrecordpes:1737en
local.publisher.placeUnited Kingdomen
local.format.startpage1en
local.format.endpage11en
local.identifier.scopusid26444482968en
local.peerreviewedYesen
local.identifier.volume5en
local.identifier.issue12en
local.access.fulltextYesen
local.contributor.lastnameEskesenen
local.contributor.lastnameEskesenen
local.contributor.lastnameKinghornen
local.contributor.lastnameRuvinskyen
dc.identifier.staffune-id:seskesenen
dc.identifier.staffune-id:bkinghoren
dc.identifier.staffune-id:aruvinsken
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.profile.roleauthoren
local.identifier.unepublicationidune:188en
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
dc.identifier.academiclevelAcademicen
local.title.maintitlePeriodicity of DNA in Exonsen
local.output.categorydescriptionC1 Refereed Article in a Scholarly Journalen
local.search.authorEskesen, STen
local.search.authorEskesen, FNen
local.search.authorKinghorn, Ben
local.search.authorRuvinsky, Aen
local.open.fileurlhttps://rune.une.edu.au/web/retrieve/c9d5d149-068e-41ff-8e90-32b73104d352en
local.uneassociationUnknownen
local.identifier.wosid000223689200001en
local.year.published2004en
local.fileurl.openhttps://rune.une.edu.au/web/retrieve/c9d5d149-068e-41ff-8e90-32b73104d352en
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