Duplication count distributions in DNA sequences.
Identifieur interne : 002029 ( PubMed/Curation ); précédent : 002028; suivant : 002030Duplication count distributions in DNA sequences.
Auteurs : Suzanne S. Sindi [États-Unis] ; Brian R. Hunt ; James A. YorkeSource :
- Physical review. E, Statistical, nonlinear, and soft matter physics [ 1539-3755 ] ; 2008.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA.
- genetics : Chromosomes, DNA.
- Animals, Base Sequence, Biophysical Phenomena, Gene Duplication, Genomics, Humans, Markov Chains, Models, Chemical, Models, Genetic, Multigene Family, Repetitive Sequences, Nucleic Acid.
Abstract
We study quantitative features of complex repetitive DNA in several genomes by studying sequences that are sufficiently long that they are unlikely to have repeated by chance. For each genome we study, we determine the number of identical copies, the "duplication count," of each sequence of length 40, that is of each "40-mer." We say a 40-mer is "repeated" if its duplication count is at least 2. We focus mainly on "complex" 40-mers, those without short internal repetitions. We find that we can classify most of the complex repeated 40-mers into two categories: one category has its copies clustered closely together on one chromosome, the other has its copies distributed widely across multiple chromosomes. For each genome and each of the categories above, we compute N(c), the number of 40-mers that have duplication count c, for each integer c. In each case, we observe a power-law-like decay in N(c) as c increases from 3 to 50 or higher. In particular, we find that N(c) decays much more slowly than would be predicted by evolutionary models where each 40-mer is equally likely to be duplicated. We also analyze an evolutionary model that does reflect the slow decay of N(c).
DOI: 10.1103/PhysRevE.78.061912
PubMed: 19256873
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Sindi</name><affiliation wicri:level="1"><nlm:affiliation>Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742, USA. suzanne_sindi@brown.edu</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742</wicri:regionArea></affiliation></author><author><name sortKey="Hunt, Brian R" sort="Hunt, Brian R" uniqKey="Hunt B" first="Brian R" last="Hunt">Brian R. Hunt</name></author><author><name sortKey="Yorke, James A" sort="Yorke, James A" uniqKey="Yorke J" first="James A" last="Yorke">James A. Yorke</name></author></analytic><series><title level="j">Physical review. 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For each genome we study, we determine the number of identical copies, the "duplication count," of each sequence of length 40, that is of each "40-mer." We say a 40-mer is "repeated" if its duplication count is at least 2. We focus mainly on "complex" 40-mers, those without short internal repetitions. We find that we can classify most of the complex repeated 40-mers into two categories: one category has its copies clustered closely together on one chromosome, the other has its copies distributed widely across multiple chromosomes. For each genome and each of the categories above, we compute N(c), the number of 40-mers that have duplication count c, for each integer c. In each case, we observe a power-law-like decay in N(c) as c increases from 3 to 50 or higher. In particular, we find that N(c) decays much more slowly than would be predicted by evolutionary models where each 40-mer is equally likely to be duplicated. We also analyze an evolutionary model that does reflect the slow decay of N(c).</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">19256873</PMID><DateCompleted><Year>2009</Year><Month>04</Month><Day>02</Day></DateCompleted><DateRevised><Year>2019</Year><Month>01</Month><Day>08</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">1539-3755</ISSN><JournalIssue CitedMedium="Print"><Volume>78</Volume><Issue>6 Pt 1</Issue><PubDate><Year>2008</Year><Month>Dec</Month></PubDate></JournalIssue><Title>Physical review. E, Statistical, nonlinear, and soft matter physics</Title><ISOAbbreviation>Phys Rev E Stat Nonlin Soft Matter Phys</ISOAbbreviation></Journal><ArticleTitle>Duplication count distributions in DNA sequences.</ArticleTitle><Pagination><MedlinePgn>061912</MedlinePgn></Pagination><Abstract><AbstractText>We study quantitative features of complex repetitive DNA in several genomes by studying sequences that are sufficiently long that they are unlikely to have repeated by chance. For each genome we study, we determine the number of identical copies, the "duplication count," of each sequence of length 40, that is of each "40-mer." We say a 40-mer is "repeated" if its duplication count is at least 2. We focus mainly on "complex" 40-mers, those without short internal repetitions. We find that we can classify most of the complex repeated 40-mers into two categories: one category has its copies clustered closely together on one chromosome, the other has its copies distributed widely across multiple chromosomes. For each genome and each of the categories above, we compute N(c), the number of 40-mers that have duplication count c, for each integer c. In each case, we observe a power-law-like decay in N(c) as c increases from 3 to 50 or higher. In particular, we find that N(c) decays much more slowly than would be predicted by evolutionary models where each 40-mer is equally likely to be duplicated. We also analyze an evolutionary model that does reflect the slow decay of N(c).</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Sindi</LastName><ForeName>Suzanne S</ForeName><Initials>SS</Initials><AffiliationInfo><Affiliation>Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742, USA. suzanne_sindi@brown.edu</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hunt</LastName><ForeName>Brian R</ForeName><Initials>BR</Initials></Author><Author ValidYN="Y"><LastName>Yorke</LastName><ForeName>James A</ForeName><Initials>JA</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>R01 HG002945-01</GrantID><Acronym>HG</Acronym><Agency>NHGRI NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>1R01HG0294501</GrantID><Acronym>HG</Acronym><Agency>NHGRI NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2008</Year><Month>12</Month><Day>11</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Phys Rev E Stat Nonlin Soft Matter Phys</MedlineTA><NlmUniqueID>101136452</NlmUniqueID><ISSNLinking>1539-3755</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base 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