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Duplication in DNA Sequences [chapter]

Masami Ito, Lila Kari, Zachary Kincaid, Shinnosuke Seki
2009 Natural Computing Series  
During DNA replication, subsequences of a strand of DNA may be copied several times (duplication) or skipped (repeat-deletion).  ...  Duplication and repeat-deletion are the basic models of errors occurring during DNA replication from the viewpoint of formal languages.  ...  Kathleen Hill for extended discussions on the biological motivation for duplication and repeat-deletion.  ... 
doi:10.1007/978-3-540-88869-7_4 fatcat:2uzs3yvhgjegbj6lqodpryvu34

Duplication count distributions in DNA sequences

Suzanne S. Sindi, Brian R. Hunt, James A. Yorke
2008 Physical Review E  
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."  ...  INTRODUCTION The term genome refers to the complete DNA sequence of an organism and is typically represented as a sequence of bases denoted A, C, G, and T.  ... 
doi:10.1103/physreve.78.061912 pmid:19256873 pmcid:PMC3121164 fatcat:3msuscezvnepncevbrwg44howq

On a chain of fragmentation equations for duplication-mutation dynamics in DNA sequences [article]

M.V. Koroteev
2015 arXiv   pre-print
Recent studies have revealed that for the majority of species the length distributions of duplicated sequences in natural DNA follow a power-law tail.  ...  We study duplication-mutation models for processes in natural DNA sequences and the length distributions of exact matches computed from both synthetic and natural sequences.  ...  INTRODUCTION In recent years a series of duplication-mutation models related to processes occurring in natural DNA sequences has been reported [1] [2] [3] .  ... 
arXiv:1501.04078v4 fatcat:kfysnmo5lnhb3hrytrilyfr6pq

DNA sequence duplications trigger gene inactivation in Neurospora crassa

E. U. Selker, P. W. Garrett
1988 Proceedings of the National Academy of Sciences of the United States of America  
Previous work showed a correlation between the occurrence of these radical changes, referred to by the acronym RIP, and the presence of sequence duplications resulting from the introduced DNA.  ...  Transforming sequences are faithfully replicated in vegetative cells ofNeurospora but are typically subject at high frequency to sequence alterations and methylation in the period between fertilization  ...  Both copies of the duplicated gene were subject to the RIP process in crosses of this strain. We conclude that sequence duplications, per se, trigger RIP.  ... 
doi:10.1073/pnas.85.18.6870 pmid:2842795 pmcid:PMC282080 fatcat:bujbyfzfpjdk7o7dwl7ou3cmxq

Nomad DNA ? A model for movement and duplication of DNA sequences in plant genomes

Eran Pichersky
1990 Plant Molecular Biology  
Thin line in parentheses ( ) indicates sequence which constitutes the 5' DR; it has sequence identity with the 3' end of the insert, but it is generated by the filling-in of the broken target DNA and is  ...  of copies of mildly duplicated sequences.  ... 
doi:10.1007/bf00019160 pmid:2103462 fatcat:f7i7as7nlzeq7dg2ynpe7vgpau

Inverted duplicate DNA sequences increase translocation rates through sequencing nanopores resulting in reduced base calling accuracy

Pieter Spealman, Jaden Burrell, David Gresham
2020 Nucleic Acids Research  
Inverted duplicate DNA sequences in both yeast and human samples were observed to have systematic elevation in the electrical current detected at the nanopore, increased translocation rates and decreased  ...  Inverted duplicated DNA sequences are a common feature of structural variants (SVs) and copy number variants (CNVs).  ...  read in the human genome.  ... 
doi:10.1093/nar/gkaa206 pmid:32255181 fatcat:xggul2ytd5e6xehodiocie2hw4

Evidence for a duplicated mitochondrial region in Audubon's shearwater based on MinION sequencing

Lucas Torres, Andreanna J. Welch, Catherine Zanchetta, R. Terry Chesser, Maxime Manno, Cécile Donnadieu, Vincent Bretagnolle, Eric Pante
2018 Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis  
Evidence suggests that part of the mitochondrial genome of Procellariiformes, especially albatrosses, is duplicated, but no DNA fragment covering the entire duplication has been sequenced.  ...  Long-read sequencing suggests heteroplasmy and a novel arrangement within the duplicated region, indicating a complex evolution of the mitogenome in Procellariiformes. ARTICLE HISTORY  ...  DNA was not sheared so as to maximize sequencing read length.  ... 
doi:10.1080/24701394.2018.1484116 pmid:30043666 fatcat:l33qd4cjnraxvcswjqmf4abk5u

Polymorphic duplicate genes and persistent non-coding sequences reveal heterogeneous patterns of mitochondrial DNA loss in salamanders

Rebecca A. Chong, Rachel Lockridge Mueller
2017 BMC Genomics  
We then analyze these gene orders in a phylogenetic context to reveal patterns of DNA loss after mitochondrial gene duplication.  ...  In addition, we show that non-coding DNA duplicated at the base of the clade has persisted across species for tens of millions of years.  ...  Non-coding sequences Two regions of non-coding, repetitive DNA remain in all Aneides mitochondrial genomes from the ancestral duplication at the base of the clade.  ... 
doi:10.1186/s12864-017-4358-2 pmid:29281973 pmcid:PMC5745709 fatcat:mnirokgfvng5rdr24j5ecyel2u

A natural case of RIP: degeneration of the DNA sequence in an ancestral tandem duplication

W S Grayburn, E U Selker
1989 Molecular and Cellular Biology  
Triplex DNA, known to occur in homopurine-homopyrimidine sequences, may have mediated the tandem duplication.  ...  Sequence analysis suggests that the xi-eta region arose from the theta region by duplication of a 794-base-pair segment followed by 267 G.C to A.T mutations in the duplicated DNA.  ...  This and the fact that DNA methylation in the ;--q vicinity appears to be limited to the duplicated sequences (E. U.  ... 
doi:10.1128/mcb.9.10.4416 pmid:2531278 pmcid:PMC362524 fatcat:kioueexugna7fp7ennpztciyxq

Tandem direct duplications of mitochondrial DNA in mitochondrial myopathy: analysis of nucleotide sequence and tissue distribution

J. Poulton, M.E. Deadman, R.M. Gardiner
1989 Nucleic Acids Research  
Two patients with direct tandem duplications of mitochondrial DNA (mtDNA) and mitochondrial myopathy are described.  ...  The brekpoint regions between duplicated segments were amplified using the polymerase chain reaction (PCR), cloned and sequenced.  ...  B Lake for kindly supplying muscle biopsy material, Prof G Attardi and Dr M King for allowing us to use the mitochondrial probes, Prof A C Wilson and associates for providing primers and instruction in  ... 
doi:10.1093/nar/17.24.10223 pmid:2602151 pmcid:PMC335296 fatcat:24dnqt7k45cknl3cvz5fsmg4bm

Specificity of repeat-induced point mutation (RIP) in Neurospora: sensitivity of non-Neurospora sequences, a natural diverged tandem duplication, and unique DNA adjacent to a duplicated region

E J Foss, P W Garrett, J A Kinsey, E U Selker
1991 Genetics  
The process designated RIP (repeat-induced point mutation) alters duplicated DNA sequences in the sexual cycle of Neurospora crassa.  ...  DNA sequence analysis of unduplicated pUC8 sequences adjacent to a duplication revealed that RIP continued at least 180 bp beyond the boundary of the duplication.  ...  Novel MboI fragments represent changes in the DNA sequence.  ... 
pmid:1827630 pmcid:PMC1204398 fatcat:xs4ebvvazrba5grz7quqkzlphy

DNA Sequence Duplication in Rhodobacter sphaeroides 2.4.1: Evidence of an Ancient Partnership between Chromosomes I and II

M. Choudhary, Y.-X. Fu, C. Mackenzie, S. Kaplan
2004 Journal of Bacteriology  
Most of the DNA sequence duplications in the R. sphaeroides genome occurred early in species history, whereas more recent sequence duplications are rarely found.  ...  To uncover the history of gene duplications in the R. sphaeroides genome, 44 gene duplications were sampled and then analyzed for DNA sequence similarity against orthologous DNA sequences.  ...  RESULTS Exact DNA duplication. The DNA sequence analysis revealed an extensive amount of exact DNA duplication within the R. sphaeroides chromosomes, as shown in Fig. 1 .  ... 
doi:10.1128/jb.186.7.2019-2027.2004 pmid:15028685 pmcid:PMC374402 fatcat:wflfdfarprb7ziekddruyz6cqe

Complete mitochondrial DNA sequence of oyster Crassostrea hongkongensis-a case of "Tandem duplication-random loss" for genome rearrangement in Crassostrea?

Ziniu Yu, Zhengpeng Wei, Xiaoyu Kong, Wei Shi
2008 BMC Genomics  
Of the 41 complete mt genomes sequenced so far, 12 are from bivalves. We determined, in the current study, the complete mitochondrial DNA sequence of Crassostrea hongkongensis.  ...  A striking finding of this study is that a DNA segment containing four tRNA genes (trnk1, trnC, trnQ1 and trnN) and two duplicated or split rRNA gene (rrnL5' and rrnS) are absent from the genome, when  ...  Unlike the 16S rRNA gene in C. gigas and C. virginica mt-DNA, it is not split or duplicated into two fragments (Fig. 2 ) [5] .  ... 
doi:10.1186/1471-2164-9-477 pmid:18847502 pmcid:PMC2576254 fatcat:dcahnbelknf3lpveq4igiyrnzy

Information transfer between duplicated chromosomal sequences in mammalian cells involves contiguous regions of DNA

R. M. Liskay, J. L. Stachelek
1986 Proceedings of the National Academy of Sciences of the United States of America  
We have investigated the nature of Information transfer that appears to occur nonreciprocally between duplicated chromosomal sequences in cultured mouse L cells.  ...  In this report, we present experiments designed to answer several related questions about the nature of information transfer between duplicated Herpes virus thymidine kinase gene sequences in mammalian  ...  In summary, we have studied gene conversion events between duplicated HSV TK sequences in mouse L cells and have found that these events appear to involve contiguous regions of DNA that are often less  ... 
doi:10.1073/pnas.83.6.1802 pmid:3006074 pmcid:PMC323172 fatcat:ow6gs6c2kngsrkrjyigi4subhe

DNA Sequence Variation at a Duplicated Gene: Excess of Replacement Polymorphism and Extensive Haplotype Structure in the Drosophila melanogasterbicoid Region

John F. Baines, Ying Chen, Aparup Das, Wolfgang Stephan
2002 Molecular biology and evolution  
In this study, DNA sequence variation was examined for a 4-kb region of the bcd gene, including a portion of the 5Ј UTR, the entire coding region, and the 3Ј UTR, for 25 Drosophila melanogaster isofemale  ...  Several studies in Drosophila and closely related insects suggest that bcd may be the result of a gene duplication in the Dipteran lineage.  ...  Acknowledgments We would like to thank Yuseob Kim and John Parsch for helpful discussions and comments on the manuscript and Jake Russell for assistance in sequencing and fly crosses.  ... 
doi:10.1093/oxfordjournals.molbev.a004179 pmid:12082119 fatcat:v2pe6idy5rdnpcqxg2fspesmzu
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