MersV1, Main, Exploration, bibRecord, 002988

Duplication count distributions in DNA sequences.

Identifieur interne : 002988 ( Main/Exploration ); précédent : 002987; suivant : 002989

Duplication count distributions in DNA sequences.

Auteurs : Suzanne S. Sindi [États-Unis] ; Brian R. Hunt ; James A. Yorke

Source :

Physical review. E, Statistical, nonlinear, and soft matter physics [ 1539-3755 ] ; 2008.

RBID : pubmed:19256873

Descripteurs français

KwdFr :
- ADN (), ADN (génétique), Animaux, Chaines de Markov, Chromosomes (génétique), Duplication de gène, Famille multigénique, Génomique, Humains, Modèles chimiques, Modèles génétiques, Phénomènes biophysiques, Séquence nucléotidique, Séquences répétées d'acides nucléiques.
MESH :
- génétique : ADN, Chromosomes.
- ADN, Animaux, Chaines de Markov, Duplication de gène, Famille multigénique, Génomique, Humains, Modèles chimiques, Modèles génétiques, Phénomènes biophysiques, Séquence nucléotidique, Séquences répétées d'acides nucléiques.

English descriptors

KwdEn :
- Animals, Base Sequence, Biophysical Phenomena, Chromosomes (genetics), DNA (chemistry), DNA (genetics), Gene Duplication, Genomics, Humans, Markov Chains, Models, Chemical, Models, Genetic, Multigene Family, Repetitive Sequences, Nucleic Acid.
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

Affiliations:

Le document en format XML

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<front><div type="abstract" xml:lang="en">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).</div>
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Serveur d'exploration MERS

Duplication count distributions in DNA sequences.

Duplication count distributions in DNA sequences.

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

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Pour générer des pages wiki

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