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Journal articles on the topic 'DNA sequences'

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Author: Grafiati

Published: 4 June 2021

Last updated: 31 January 2023

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1

He, Ping-an, and Jun Wang. "Characteristic Sequences for DNA Primary Sequence." Journal of Chemical Information and Computer Sciences 42, no. 5 (September 2002): 1080–85. http://dx.doi.org/10.1021/ci010131z.

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2

AUFFRAY, CHARLES. "DNA sequences." Nature 355, no. 6358 (January 1992): 292. http://dx.doi.org/10.1038/355292b0.

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3

Yablonsky, Michael D., and William J. Hone. "Patenting DNA Sequences." Nature Biotechnology 13, no. 7 (July 1995): 656–57. http://dx.doi.org/10.1038/nbt0795-656.

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4

King, D. G., and Y. Kashi. "Heretical DNA Sequences?" Science 326, no. 5950 (October 8, 2009): 229–30. http://dx.doi.org/10.1126/science.326_229.

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5

Hoss, Matthias, Svante Paabo, and N. K. Vereshchagin. "Mammoth DNA sequences." Nature 370, no. 6488 (August 1994): 333. http://dx.doi.org/10.1038/370333a0.

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6

Agris, Cheryl H. "Patenting DNA sequences." Nature Biotechnology 16, no. 9 (September 1998): 877. http://dx.doi.org/10.1038/nbt0998-877.

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7

Chen, William Y. C., and James D. Louck. "Necklaces, MSS Sequences, and DNA Sequences." Advances in Applied Mathematics 18, no. 1 (January 1997): 18–32. http://dx.doi.org/10.1006/aama.1996.0494.

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8

Churchill, Gary A., and Michael S. Waterman. "The accuracy of DNA sequences: Estimating sequence quality." Genomics 14, no. 1 (September 1992): 89–98. http://dx.doi.org/10.1016/s0888-7543(05)80288-5.

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9

He, Ping-an, and Jun Wang. "ChemInform Abstract: Characteristic Sequences for DNA Primary Sequence." ChemInform 33, no. 47 (May 19, 2010): no. http://dx.doi.org/10.1002/chin.200247209.

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10

Onozawa, Masahiro, Tamas Varga, Yoo Jung Kim, Zhenhua Zhang, and Peter Aplan. "Repair of DNA Double Strand Breaks by RNA/DNA Patches in U937 Cells." Blood 120, no. 21 (November 16, 2012): 2375. http://dx.doi.org/10.1182/blood.v120.21.2375.2375.

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Abstract Abstract 2375 It has been suggested that errors in the repair of DNA double strand breaks (DSB) can result in gross chromosomal rearrangements (GCR), including chromosomal amplifications, deletions, inversions, and translocations. To study repair of DNA DSB in vivo, we generated a vector containing the EF1a promoter driving expression of the herpes simplex thymidine kinase (HsTK); interspersed between the EF1a promoter and Hstk cDNA was the recognition site for the rare-cutting meganuclease I-SceI. This vector was electroporated into U937 cells, and a clone containing a single copy, of the EF1aTK vector, designated F5, was isolated. Transfection of the F5 cells with an I-SceI expression vector, followed by ganciclovir selection, identified clones that had lost expression of HsTK. We recovered no GCR with this approach; most of the GCV-resistant clones had partial or complete deletions of the EF1a promoter, the HsTK cDNA, or both. However we noted that ∼5–10% of repair elements involved insertions of DNA sequences derived from distant regions of the genome; the length of the inserted fragment varied from 47 to 756 bp. Surprisingly, all of the inserted fragments were derived from gene and/or retrotransposon repeat elements such as LINE (Long Interspersed Nuclear Element) or SINE (Short Interspersed Nuclear Element) sequences. Therefore, we hypothesized that the inserted sequences used to “patch” the DNA DSB could be based on reverse transcription of an RNA template. Since sequences derived from human RNA and human genomic DNA are identical (with the exception of RNA splice events, poly-A tails, and RNA-edited nucleotides), we co-transfected the F5 cells with murine RNA and an I-SceI expression vector to test the hypothesis that the patches at the DNA DSB sites could be derived from RNA. After hygromycin selection for successfully transfected cells, genomic DNA was isolated, and amplified with primers that flanked the I-SceI cleavage site. DNA fragments of 500–1000bp (larger than the size of the uncleaved EF!aTK PCR product, which was 400 bp) containing insertions at the I-SceI site were isolated, subcloned, and sequenced. We identified 51 independent sequences which had insertions of 23–266 bp at I-SceI cleavage site. Of these 51 insertions, 4 were vector capture events (derived form the expression vector), and 4 were too short to identify unambiguously. Of the remaining 43 insertions, 39 were derived from a single genomic loci, and 4 samples contained identifiable sequences from 2 distinct genomic regions. The sequences were derived from 16 of the 24 human chromosomes, with no clear preference for any specific chromosome. 62% of the sequences were found to contain sequences from a transcribed gene region, and 64% contained repeat sequences such as LINE, SINE, or LTR. The involvement of retrotransposon sequences, which are known to be reverse transcribed and integrated into the genome, supports the hypothesis that at least some of the insertions may be templated from RNA. Furthermore, 45 of the 47 inserted sequences were derived from endogenous human sequences; however 2 insertions matched to mouse sequences, and were derived from the co-transfected mouse RNA. One sample matched an intronic region of murine Vwa3b, which we confirmed was highly expressed in the mouse cells used to harvest the RNA used for the co-transfection. A second sample was not a gene sequence but contained a LINE element. Taken together, these findings demonstrate that I-SceI-induced DNA DSB can be repaired by “patches” derived from distant regions of the genome. This is the first systematic study focused on captured sequences at DNA DSB sites in the mammalian genome, and suggests that transcribed mRNA and retrotransposons can play an important role in the repair of DNA DSB and preservation of genomic integrity. Finally, the observation that I-SceI-induced DNA DSBs are often repaired by insertions suggests that these insertions could be mistaken for chromosome translocations, if only one “side” of the DNA DSB is sequenced. Disclosures: No relevant conflicts of interest to declare.

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11

Pearson, William R., Todd Wood, Zheng Zhang, and Webb Miller. "Comparison of DNA Sequences with Protein Sequences." Genomics 46, no. 1 (November 1997): 24–36. http://dx.doi.org/10.1006/geno.1997.4995.

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12

AVRAMOVA, ZOYA, OLEG GEORGIEV, and ROUMEN TSANEV. "DNA Sequences Tightly Bound to Proteins in Mouse Chromatin: Identification of Murine MER Sequences." DNA and Cell Biology 13, no. 5 (May 1994): 539–48. http://dx.doi.org/10.1089/dna.1994.13.539.

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13

Weir, BS. "Analysis of DNA sequences." Statistical Methods in Medical Research 2, no. 3 (November 1993): 225–39. http://dx.doi.org/10.1177/096228029300200303.

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14

Wisecarver, James. "Amplification of DNA Sequences." Laboratory Medicine 28, no. 3 (March 1, 1997): 191–95. http://dx.doi.org/10.1093/labmed/28.3.191.

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15

Cattani, Carlo, and CRita D'Auria. "Correlations in DNA sequences." Journal of Information and Optimization Sciences 28, no. 1 (January 2007): 51–65. http://dx.doi.org/10.1080/02522667.2007.10699728.

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16

Richards, Robert I., and Grant R. Sutherland. "Heritable unstable DNA sequences." Nature Genetics 1, no. 1 (April 1992): 7–9. http://dx.doi.org/10.1038/ng0492-7.

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17

McGuire, Gráinne, Michael C. Denham, and David J. Balding. "Models of Sequence Evolution for DNA Sequences Containing Gaps." Molecular Biology and Evolution 18, no. 4 (April 1, 2001): 481–90. http://dx.doi.org/10.1093/oxfordjournals.molbev.a003827.

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18

Binns, Matthew. "Contamination of DNA database sequence entries withEscherichia coliinsertion sequences." Nucleic Acids Research 21, no. 3 (1993): 779. http://dx.doi.org/10.1093/nar/21.3.779.

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19

Gabrielian, Andrei, Kristian Vlahovicek, and Sándor Pongor. "Distribution of sequence-dependent curvature in genomic DNA sequences." FEBS Letters 406, no. 1-2 (April 7, 1997): 69–74. http://dx.doi.org/10.1016/s0014-5793(97)00236-6.

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20

Bell, George I., and David C. Torney. "Repetitive DNA sequences: Some considerations for simple sequence repeats." Computers & Chemistry 17, no. 2 (June 1993): 185–90. http://dx.doi.org/10.1016/0097-8485(93)85009-2.

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21

Mulia, Sudipta, Debahuti Mishra, and Tanushree Jena. "Profile HMM based Multiple Sequence Alignment for DNA Sequences." Procedia Engineering 38 (2012): 1783–87. http://dx.doi.org/10.1016/j.proeng.2012.06.218.

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22

Li, Dawei, Zhaoqi Yang, Guanjia Zhao, Yi Long, Bei Lv, Cheng Li, Shuhui Hiew, et al. "Manipulating DNA writhe through varying DNA sequences." Chemical Communications 47, no. 26 (2011): 7479. http://dx.doi.org/10.1039/c1cc11543j.

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23

Murray, Vincent, and Niruba Kandasamy. "The Sequence Specificity of the Anti-tumour Drug, Cisplatin, in Telomeric DNA Sequences Compared with Consecutive Guanine DNA Sequences." Anti-Cancer Agents in Medicinal Chemistry 12, no. 3 (March 1, 2012): 177–81. http://dx.doi.org/10.2174/187152012800228742.

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24

LUNDEBERG, JOAKIM, JOHAN WAHLBERG, MARTIN HOLMBERG, ULF PETTERSSON, and MATHIAS UHLÉN. "Rapid Colorimetric Detection ofIn VitroAmplified DNA Sequences." DNA and Cell Biology 9, no. 4 (May 1990): 287–92. http://dx.doi.org/10.1089/dna.1990.9.287.

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25

Ali, Mashooq, Noshin Afshan, Chuan Jiang, Hongning Zheng, and Shou-Jun Xiao. "2D DNA lattice arrays assembled from DNA dumbbell tiles using poly(A-T)-rich stems." Nanoscale 11, no. 46 (2019): 22216–21. http://dx.doi.org/10.1039/c9nr07911d.

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Poly(A-T)-rich sequences as stems of DNA dumbbell tiles have been evidenced to be more rigid than randomly-sequenced stems for construction of single crystalline 2D lattice arrays with sub-tiles resolved by AFM in slightly acidic solutions.

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26

Kauffman, D. L., P. J. Keller, A. Bennick, and M. Blum. "Alignment of Amino Acid and DNA Sequences of Human Proline-rich Proteins." Critical Reviews in Oral Biology & Medicine 4, no. 3 (April 1993): 287–92. http://dx.doi.org/10.1177/10454411930040030501.

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Human proline-rich proteins (PRPs) constitute a complex family of salivary proteins that are encoded by a small number of genes. The primary gene product is cleaved by proteases, thereby giving rise to about 20 secreted proteins. To determine the genes for the secreted PRPs, therefore, it is necessary to obtain sequences of both the secreted proteins and the DNA encoding these proteins. We have sequenced most PRPs from one donor (D.K.) and aligned the protein sequences with available DNA sequences from unrelated individuals. Partial sequence data have now been obtained for an additional PRP from D.K. named II-1. This protein was purified from parotid saliva by gel filtration and ion-exchange chromatography. Peptides were obtained by cleavage with trypsin, clostripain, and N-bromosuccinimide, followed by column chromatography. The peptides were sequenced on a gas-phase protein sequenator. Overlapping peptide sequences were obtained for most of II-1 and aligned with translated DNA sequences. The best fit was obtained with clones containing sequences for the allele PRB4" (Lyons et al., 1988). However, there was not complete identity of the protein amino acid sequence and the DNA-derived sequences, indicating that II-1 is not encoded by PRB4". Other PRPs isolated from D.K. also fail to conform to any DNA structure so far reported. This shows the need to obtain amino acid sequences and corresponding DNA sequences from the same person to assign genes for the PRPs and to determine the location of the postribosomal cleavage points in the primary translation product.

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27

Fatchiyah, Fatchiyah, Rista Nikmatu Rohmah, Lidwina Faraline Tripisila, Dewi Ratih Tirto Sari, Adelia Adrianne Tapiory, Jihan Safira Ainnayah, Viona Faiqoh, Fajar Mustika Alam, and Ahmad Faizal Abdul Razis. "Three-dimension Glyceraldehyde-3-Phosphate Dehydrogenase protein structure of substitution and insertion sequences of GAPDH gene of chicken drumstick meat (Gallus gallus)." Berkala Penelitian Hayati 27, no. 2 (April 5, 2022): 105–9. http://dx.doi.org/10.23869/bphjbr.27.2.20228.

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The study aimed to observed the 3-D structure of GAPDH protein and identify the GAPDH gene sequences mutation of chicken drumstick meat (Gallus gallus). The sample of chicken meat was randomly taken in four districts in Malang city. In this study, the DNA was isolated from drumstick meat chicken samples, amplified using proper primers, and then sequenced using ABI 3730xl DNA Sequencer. The DNA sequences alignments analyzed by BioEdit software and the control sequence of GAPDH gene was obtained from NCBI GenBank (sequence Gene ID: 374193). Then, the amino acid sequence and 3D structure of GAPDH protein were determined based on the change of nucleotide sequences using Swiss model and PyMol software. The nucleotide sequence of a partially GAPDH gene of drumstick meat chicken from districts two is completely different with a 97 percent similarity level, which found twelve nucleotides’ substitutions mutation between nucleotide base number 354 until 777 and three nucleotides inserted between T753 and G754 nucleotide base. These mutations changed the amino acid sequence and 3D structure of GAPDH protein. This result suggests that the differential drumstick chicken meat GAPDH sequences and 3D structure may induce the change of protein-protein interaction and induction.

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28

Leng, Rhodri, Gil Viry, Miguel García-Sancho, James Lowe, Mark Wong, and Niki Vermeulen. "The Sequences and the Sequencers." Historical Studies in the Natural Sciences 52, no. 3 (June 1, 2022): 277–319. http://dx.doi.org/10.1525/hsns.2022.52.3.277.

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This special issue on sequences and sequencers uses new analytical approaches to re-assess the history of genomics. Historical attention has largely focused on a few central characters and institutions: those that participated in the Human Genome Project (HGP), especially its final stages. Our analysis—based on an assessment of almost 13.5 million DNA sequence submissions and 30,000 publications of human, yeast, and pig DNA sequences—followed overlapping chronologies starting before and finishing after the concerted efforts to sequence the genomes of each species: 1980 to 2000 in yeast, 1985 to 2005 for the human, and 1990 to 2015 for the pig. Our main conclusion is that when broader sequencing practices—especially those addressed to nonhuman species—are taken into account, the large-scale center model that characterized the organization of the HGP falls short in representing genomics as a whole. Instead of taking the HGP as a model, we describe an iterative process in which the practices of sequence submission and publication were entangled. Analysis of co-authorship networks between institutions derived from our data shows how linked sequence submission and publication were to medical, biochemical, and agricultural research. Our analysis thus reveals the utility of big data and mixed-methods approaches for addressing science as a multidimensional endeavor with a history shaped by co-constitutive, synchronic interactions among different elements—such as communities, species, and disciplines—as much as diachronic trajectories over time. This perspective enables us to better capture interdisciplinary and interspecies work, and offers a more fluid portrayal of the connections between scientific practices and agricultural, industrial, and medical goals. This essay is part of a special issue entitled The Sequences and the Sequencers: A New Approach to Investigating the Emergence of Yeast, Human, and Pig Genomics, edited by Michael García-Sancho and James Lowe.

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29

Harrington, Colleen T., Elaine I. Lin, Matthew T. Olson, and James R. Eshleman. "Fundamentals of Pyrosequencing." Archives of Pathology & Laboratory Medicine 137, no. 9 (September 1, 2013): 1296–303. http://dx.doi.org/10.5858/arpa.2012-0463-ra.

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Context.—DNA sequencing is critical to identifying many human genetic disorders caused by DNA mutations, including cancer. Pyrosequencing is less complex, involves fewer steps, and has a superior limit of detection compared with Sanger sequencing. The fundamental basis of pyrosequencing is that pyrophosphate is released when a deoxyribonucleotide triphosphate is added to the end of a nascent strand of DNA. Because deoxyribonucleotide triphosphates are sequentially added to the reaction and because the pyrophosphate concentration is continuously monitored, the DNA sequence can be determined. Objective.—To demonstrate the fundamental principles of pyrosequencing. Data Sources.—Salient features of pyrosequencing are demonstrated using the free software program Pyromaker (http://pyromaker.pathology.jhmi.edu), through which users can input DNA sequences and other pyrosequencing parameters to generate the expected pyrosequencing results. Conclusions.—We demonstrate how mutant and wild-type DNA sequences result in different pyrograms. Using pyrograms of established mutations in tumors, we explain how to analyze the pyrogram peaks generated by different dispensation sequences. Further, we demonstrate some limitations of pyrosequencing, including how some complex mutations can be indistinguishable from single base mutations. Pyrosequencing is the basis of the Roche 454 next-generation sequencer and many of the same principles also apply to the Ion Torrent hydrogen ion-based next-generation sequencers.

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30

McKinnon, Christian, and Guy Drouin. "Chromatin diminution in the copepod Mesocyclops edax: elimination of both highly repetitive and nonhighly repetitive DNA." Genome 56, no. 1 (January 2013): 1–8. http://dx.doi.org/10.1139/gen-2012-0097.

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Chromatin diminution, a developmentally regulated process of DNA elimination, is found in numerous eukaryotic species. In the copepod Mesocyclops edax, some 90% of its genomic DNA is eliminated during the differentiation of embryonic cells into somatic cells. Previous studies have shown that the eliminated DNA contains highly repetitive sequences. Here, we sequenced DNA fragments from pre- and postdiminution cells to determine whether nonhighly repetitive sequences are also eliminated during the process of chromatin diminution. Comparative analyses of these sequences, as well as the sequences eliminated from the genome of the copepod Cyclops kolensis, show that they all share similar abundances of tandem repeats, dispersed repeats, transposable elements, and various coding and noncoding sequences. This suggests that, in the chromatin diminution observed in M. edax, both highly repetitive and nonhighly repetitive sequences are eliminated and that there is no bias in the type of nonhighly repetitive DNA being eliminated.

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31

Wang, Yanfeng, Ruihui Shi, Zicheng Wang, Xuncai Zhang, and Guangzhao Cui. "Design of DNA Sequences for Stable DNA Tile." Journal of Bionanoscience 7, no. 3 (June 1, 2013): 265–70. http://dx.doi.org/10.1166/jbns.2013.1132.

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32

Hashimoto, Chikara, and Hisao Fujisawa. "DNA sequences necessary for packaging bacteriophage T3 DNA." Virology 187, no. 2 (April 1992): 788–95. http://dx.doi.org/10.1016/0042-6822(92)90480-d.

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33

XODO, Luigi E., Marianna ALUNNI-FABBRONI, Giorgio MANZINI, and Franco QUADRIFOGLIO. "Sequence-specific DNA-triplex formation at imperfect homopurine-homopyrimidine sequences within a DNA plasmid." European Journal of Biochemistry 212, no. 2 (March 1993): 395–401. http://dx.doi.org/10.1111/j.1432-1033.1993.tb17674.x.

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34

Vences, Miguel, Dominik Stützer, Noromalala Rasoamampionona Raminosoa, and Thomas Ziegler. "Towards a DNA barcode library for Madagascar’s threatened ichthyofauna." PLOS ONE 17, no. 8 (August 11, 2022): e0271400. http://dx.doi.org/10.1371/journal.pone.0271400.

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In order to improve the molecular resources available for conservation management of Madagascar’s threatened ichthyofauna, we elaborated a curated database of 2860 mitochondrial sequences of the mitochondrial COI, 16S and ND2 genes of Malagasy fishes, of which 1141 sequences of freshwater fishes were newly sequenced for this data set. The data set is mostly composed of COI (2015 sequences) while 16S and ND2 sequences from partly the same samples were used to match the COI sequences to reliably identified reference sequences of these genes. We observed COI uncorrected pairwise genetic distances of 5.2‒31.0% (mean 20.6%) among species belonging to different genera, and 0.0‒22.4% (mean 6.4%) for species belonging to the same genus. Deeply divergent mitochondrial lineages of uncertain attribution were found among Malagasy freshwater eleotrids and gobiids, confirming these groups are in need of taxonomic revision. DNA barcodes assigned to introduced cichlids (tilapias) included Coptodon rendallii, C. zillii, Oreochromis aureus (apparently a new country record), O. cf. mossambicus, O. niloticus, and one undetermined species of Oreochromis, with sequences of up to three species found per location. In aplocheiloid killifishes of the genus Pachypanchax, most species from northern Madagascar had only low mitochondrial divergences, three of these species (P. omalonotus, P. patriciae, and P. varatraza) were not reciprocally monophyletic, and one genetically deviant lineage was discovered in a northern locality, suggesting a need for partial taxonomic revision of this genus. While the lack of voucher specimens for most of the samples sequenced herein precludes final conclusions, our first step towards a DNA barcoding reference library of Madagascar’s fishes already demonstrates the value of such a data set for improved taxonomic inventory and conservation management. We strongly suggest further exploration of Madagascar’s aquatic environments, which should include detailed photographic documentation and tissue sampling of large numbers of specimens, and collection of preserved voucher specimens as well as of living fish for the buildup of ex situ assurance populations of threatened species complying with the One Plan Approach proposed by the IUCN SSC Conservation Breeding Specialist Group (CBSG).

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35

Karlin, S., and G. Ghandour. "Comparative statistics for DNA and protein sequences: single sequence analysis." Proceedings of the National Academy of Sciences 82, no. 17 (September 1, 1985): 5800–5804. http://dx.doi.org/10.1073/pnas.82.17.5800.

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36

Karlin, S., and G. Ghandour. "Comparative statistics for DNA and protein sequences: multiple sequence analysis." Proceedings of the National Academy of Sciences 82, no. 18 (September 1, 1985): 6186–90. http://dx.doi.org/10.1073/pnas.82.18.6186.

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37

Szalanski, Allen L., and Carrie B. Owens. "Sequence Change and Phylogenetic Signal in Muscoid COII DNA Sequences." DNA Sequence 14, no. 4 (July 2003): 331–34. http://dx.doi.org/10.1080/1085566031000141144.

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38

Wu, Paula, Ngai Fong Law, and Wan Chi Siu. "Analysis of cross sequence similarities for multiple DNA sequences compression." International Journal of Computer Aided Engineering and Technology 1, no. 4 (2009): 437. http://dx.doi.org/10.1504/ijcaet.2009.028551.

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39

Beck, Julia, Howard B. Urnovitz, Joachim Riggert, Mario Clerici, and Ekkehard Schütz. "Profile of the Circulating DNA in Apparently Healthy Individuals." Clinical Chemistry 55, no. 4 (April 1, 2009): 730–38. http://dx.doi.org/10.1373/clinchem.2008.113597.

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Abstract Background: Circulating nucleic acids (CNAs) have been shown to have diagnostic utility in human diseases. The aim of this study was to sequence and organize CNAs to document typical profiles of circulating DNA in apparently healthy individuals. Methods: Serum DNA from 51 apparently healthy humans was extracted, amplified, sequenced via pyrosequencing (454 Life Sciences/Roche Diagnostics), and categorized by (a) origin (human vs xenogeneic), (b) functionality (repeats, genes, coding or noncoding), and (c) chromosomal localization. CNA results were compared with genomic DNA controls (n = 4) that were subjected to the identical procedure. Results: We obtained 4.5 × 105 sequences (7.5 × 107 nucleotides), of which 87% were attributable to known database sequences. Of these sequences, 97% were genomic, and 3% were xenogeneic. CNAs and genomic DNA did not differ with respect to sequences attributable to repeats, genes, RNA, and protein-coding DNA sequences. CNA tended to have a higher proportion of short interspersed nuclear element sequences (P = 0.1), of which Alu sequences were significant (P < 0.01). CNAs had a significantly lower proportion of L1 and L2 long interspersed nuclear element sequences (P < 0.01). In addition, hepatitis B virus (HBV) genotype F sequences were found in an individual accidentally evaluated as a healthy control. Conclusions: Comparison of CNAs with genomic DNA suggests that nonspecific DNA release is not the sole origin for CNAs. The CNA profiling of healthy individuals we have described, together with the detailed biometric analysis, provides the basis for future studies of patients with specific diseases. Furthermore, the detection of previously unknown HBV infection suggests the capability of this method to uncover occult infections.

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40

Nagai, N., K. Kuwata, and S. Era. "Self-similarity in DNA sequences." Seibutsu Butsuri 39, supplement (1999): S202. http://dx.doi.org/10.2142/biophys.39.s202_2.

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41

Ghosh, Shubha. "Nature, nurture and DNA sequences." Pharmaceutical Patent Analyst 3, no. 1 (January 2014): 5–7. http://dx.doi.org/10.4155/ppa.13.66.

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42

Lower, Sarah E., Anne-Marie Dion-Côté, Andrew G. Clark, and Daniel A. Barbash. "Special Issue: Repetitive DNA Sequences." Genes 10, no. 11 (November 6, 2019): 896. http://dx.doi.org/10.3390/genes10110896.

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Repetitive DNAs are ubiquitous in eukaryotic genomes and, in many species, comprise the bulk of the genome. Repeats include transposable elements that can self-mobilize and disperse around the genome and tandemly-repeated satellite DNAs that increase in copy number due to replication slippage and unequal crossing over. Despite their abundance, repetitive DNAs are often ignored in genomic studies due to technical challenges in identifying, assembling, and quantifying them. New technologies and methods are now allowing unprecedented power to analyze repetitive DNAs across diverse taxa. Repetitive DNAs are of particular interest because they can represent distinct modes of genome evolution. Some repetitive DNAs form essential genome structures, such as telomeres and centromeres, that are required for proper chromosome maintenance and segregation, while others form piRNA clusters that regulate transposable elements; thus, these elements are expected to evolve under purifying selection. In contrast, other repeats evolve selfishly and cause genetic conflicts with their host species that drive adaptive evolution of host defense systems. However, the majority of repeats likely accumulate in eukaryotes in the absence of selection due to mechanisms of transposition and unequal crossing over. However, even these “neutral” repeats may indirectly influence genome evolution as they reach high abundance. In this Special Issue, the contributing authors explore these questions from a range of perspectives.

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43

Kirkwood, T. B. L., and M. S. Waterman. "Mathematical Methods for DNA Sequences." Biometrics 46, no. 3 (September 1990): 882. http://dx.doi.org/10.2307/2532117.

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44

Aram, Vahid, Ali Iranmanesh, and Z. A. Majid. "Spider Representation of DNA Sequences." Journal of Computational and Theoretical Nanoscience 11, no. 2 (February 1, 2014): 418–20. http://dx.doi.org/10.1166/jctn.2014.3371.

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45

Lenstra, J. A. "Bovine sequences in rodent DNA." Nucleic Acids Research 20, no. 11 (1992): 2892. http://dx.doi.org/10.1093/nar/20.11.2892.

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46

Salzberg, S. L. "Gene discovery in DNA sequences." IEEE Intelligent Systems 14, no. 6 (November 1999): 44–48. http://dx.doi.org/10.1109/5254.809567.

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Salzberg, Steven L. "Reminder to deposit DNA sequences." Nature 533, no. 7602 (May 2016): 179. http://dx.doi.org/10.1038/533179a.

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Uetz, Peter, and Akhil Garg. "Species disconnected from DNA sequences." Nature 545, no. 7655 (May 2017): 412. http://dx.doi.org/10.1038/545412c.

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Blaxter, M., A. Danchin, B. Savakis, K. Fukami-Kobayashi, K. Kurokawa, S. Sugano, R. J. Roberts, S. L. Salzberg, and C. I. Wu. "Reminder to deposit DNA sequences." Science 352, no. 6287 (May 11, 2016): 780. http://dx.doi.org/10.1126/science.aaf7672.

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Weir, B. S. "Mathematical analysis of DNA sequences." Genome 31, no. 2 (January 15, 1989): 1093–94. http://dx.doi.org/10.1139/g89-191.

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