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Journal articles on the topic 'DNA Fragment Assembly'

Author: Grafiati

Published: 4 June 2025

Last updated: 1 August 2025

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1

Colloms, Sean D., Christine A. Merrick, Femi J. Olorunniji, et al. "Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination." Nucleic Acids Research 42, no. 4 (2013): e23-e23. http://dx.doi.org/10.1093/nar/gkt1101.

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Abstract Synthetic biology requires effective methods to assemble DNA parts into devices and to modify these devices once made. Here we demonstrate a convenient rapid procedure for DNA fragment assembly using site-specific recombination by ϕC31 integrase. Using six orthogonal attP/attB recombination site pairs with different overlap sequences, we can assemble up to five DNA fragments in a defined order and insert them into a plasmid vector in a single recombination reaction. ϕC31 integrase-mediated assembly is highly efficient, allowing production of large libraries suitable for combinatorial

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2

Rathee, Manisha, and T. V. Vijay Kumar. "DNA Fragment Assembly Using Multi-Objective Genetic Algorithms." International Journal of Applied Evolutionary Computation 5, no. 3 (2014): 84–108. http://dx.doi.org/10.4018/ijaec.2014070105.

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DNA Fragment Assembly Problem (FAP) is concerned with the reconstruction of the target DNA, using the several hundreds (or thousands) of sequenced fragments, by identifying the right order and orientation of each fragment in the layout. Several algorithms have been proposed for solving FAP. Most of these have solely dwelt on the single objective of maximizing the sum of the overlaps between adjacent fragments in order to optimize the fragment layout. This paper aims to formulate this FAP as a bi-objective optimization problem, with the two objectives being the maximization of the overlap betwe

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Adithya B. and Santhi G. "DNA Cryptography Using DNA Fragment Assembly and Fragment Key Expansion for Genomic Data." International Journal of Organizational and Collective Intelligence 12, no. 2 (2022): 1–19. http://dx.doi.org/10.4018/ijoci.286173.

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This research proposes a tweaked scheme based on DNA fragment assembly to improve protection over insecure channel. The proposed procedure utilizes binary coding to change over an underlying plaintext into a reference DNA arrangement to deal with the fragmentation. DNA fragment key expansion is applied over the reference DNA sequence to make the short-chain fragments. The redundancy in the long-chain of reference DNA is removed using DNA fragment assembly. A look-up table is generated to store the binary values of overlapped fragments to be reassembled during the encryption and decryption proc

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4

Gheraibia, Youcef, Abdelouahab Moussaoui, Sohag Kabir, and Smaine Mazouzi. "Pe-DFA." International Journal of Applied Metaheuristic Computing 7, no. 2 (2016): 58–70. http://dx.doi.org/10.4018/ijamc.2016040104.

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DNA Fragment Assembly (DFA) is a process of finding the best order and orientation of a set of DNA fragments to reconstruct the original DNA sequence from them. As it has to consider all possible combinations among the DNA fragments, it is considered as a combinatorial optimisation problem. This paper presents a method showing the use of Penguins Search Optimisation Algorithm (PeSOA) for DNA fragment assembly problem. Penguins search optimisation is a nature inspired metaheuristic algorithm based on the collaborative hunting strategy of penguins. The approach starts its operation by generating

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5

ANGELERI, E., B. APOLLONI, D. DE FALCO, and L. GRANDI. "DNA FRAGMENT ASSEMBLY USING NEURAL PREDICTION TECHNIQUES." International Journal of Neural Systems 09, no. 06 (1999): 523–44. http://dx.doi.org/10.1142/s0129065799000563.

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The paper describes an alternative approach to the fragment assembly problem. The key idea is to train a recurrent neural network to tracking the sequence of bases constituting a given fragment and to assign to a same cluster all the sequences which are well tracked by this network. We make use of a 3-layer Recurrent Perceptron and examine both edited sequences from a ftp site and artificial fragments from a common simulation software: the clusters we obtain exhibit interesting properties in terms of error filtering, stability and self consistency; we define as well, with a certain degree of a

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6

Semashko, T. A., G. Y. Fisunov, E. A. Tsoy, et al. "Modern Approaches to de novo Synthesis of Extended DNA Fragments: Assembly of a Wide Repertoire of Sequences." Acta Naturae 16, no. 1 (2024): 77–85. http://dx.doi.org/10.32607/actanaturae.27362.

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The standardization of DNA fragment assembly methods for many tasks of synthetic biology is crucial. This is necessary for synthesizing a wider repertoire of sequences, as well as for further automation and miniaturization of such reactions. In this work, we proposed conditions for the assembly of DNA fragments from chemically synthesized oligonucleotides and we identified the errors occurring in the sequence under these conditions. Additionally, we proposed conditions for further combining synthetic fragments into larger DNA fragments. We showed that the optimized conditions are suitable for

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7

Yang, Kun, Giovanni Stracquadanio, Jingchuan Luo, Jef D. Boeke, and Joel S. Bader. "BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts." Bioinformatics 32, no. 6 (2015): 937–39. http://dx.doi.org/10.1093/bioinformatics/btv664.

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Abstract Summary: Combinatorial assembly of DNA elements is an efficient method for building large-scale synthetic pathways from standardized, reusable components. These methods are particularly useful because they enable assembly of multiple DNA fragments in one reaction, at the cost of requiring that each fragment satisfies design constraints. We developed BioPartsBuilder as a biologist-friendly web tool to design biological parts that are compatible with DNA combinatorial assembly methods, such as Golden Gate and related methods. It retrieves biological sequences, enforces compliance with a

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8

Beeram, Satyanarayana Reddy, and Edara Srinivasa Reddy. "A Study of DNA Fragment Assembly Algorithms." Journal of Applied Physics and Engineering 1, no. 1 (2016): 10–16. http://dx.doi.org/10.26524/jap2.

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9

Raja, G., and U. Srinivasulu Reddy. "DNA Fragment Assembly Using Hybridized Catfish PSO." International Journal of Software Innovation 9, no. 2 (2021): 69–80. http://dx.doi.org/10.4018/ijsi.2021040104.

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DNA fragment assembly aids in uncovering several aspects of the human DNA, and hence in-turn enables scientists in understanding and curing several hereditary problems. Several computational methods have been proposed to solve this problem. However, the huge size and the NP-hard nature of the problem poses several challenges in proposing a time effective system for fragment assembly. This paper proposes a hybridized catfish PSO model for the process of fragment assembly. PSO algorithm is enhanced by incorporating the catfish particles to enable the model to get out of the local optimal solutio

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10

Quiroz-Ibarra, J., Guillermo Mallén-Fullerton, and Guillermo Fernández-Anaya. "DNA Paired Fragment Assembly Using Graph Theory." Algorithms 10, no. 2 (2017): 36. http://dx.doi.org/10.3390/a10020036.

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11

Parsons, Rebecca J., Stephanie Forrest, and Christian Burks. "Genetic algorithms, operators, and DNA fragment assembly." Machine Learning 21, no. 1-2 (1995): 11–33. http://dx.doi.org/10.1007/bf00993377.

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12

Ahmad, Sk Syeed. "DNA Fragment Assembly using Deep Recurrent Neural Network." International Journal for Research in Applied Science and Engineering Technology 8, no. 5 (2020): 1142–49. http://dx.doi.org/10.22214/ijraset.2020.5181.

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13

Pevzner, P. A., H. Tang, and M. S. Waterman. "An Eulerian path approach to DNA fragment assembly." Proceedings of the National Academy of Sciences 98, no. 17 (2001): 9748–53. http://dx.doi.org/10.1073/pnas.171285098.

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14

Fullerton, Guillermo M. Mallén, James Alexander Hughes, Sheridan Houghten, and Guillermo Fernández Anaya. "Benchmark datasets for the DNA fragment assembly problem." International Journal of Bio-Inspired Computation 5, no. 6 (2013): 384. http://dx.doi.org/10.1504/ijbic.2013.058912.

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15

ALBA, Enrique. "An efficient discrete PSO coupled with a fast local search heuristic for the DNA fragment assembly problem." Information Sciences 512 (June 7, 2019): 880–908. https://doi.org/10.1016/j.ins.2019.10.026.

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This paper focuses on Particle Swarm Optimization (PSO) applied to the DNA fragment as- sembly problem. Existing PSO algorithms for this permutation-based combinatorial prob- lem use the Smaller Position Value (SPV) rule to transform continuous vectors into permu- tations of integers. However, this approach has limitations and is not suitable for this NP- hard problem. Here we propose a new discrete PSO that works directly in the search space of permutations and effectively addresses the fragment assembly problem. In our proposal, the fact that relative ordering of DNA fragments is most indica

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16

Hermans, Armand P. H. M., Tjakko Abee, Marcel H. Zwietering, and Henk J. M. Aarts. "Identification of Novel Salmonella enterica Serovar Typhimurium DT104-Specific Prophage and Nonprophage Chromosomal Sequences among Serovar Typhimurium Isolates by Genomic Subtractive Hybridization." Applied and Environmental Microbiology 71, no. 9 (2005): 4979–85. http://dx.doi.org/10.1128/aem.71.9.4979-4985.2005.

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ABSTRACT Genomic subtractive hybridization was performed between Salmonella enterica serovar Typhimurium LT2 and DT104 to search for novel Salmonella serovar Typhimurium DT104-specific sequences. The subtraction resulted mainly in the isolation of DNA fragments with sequence similarity to phages. Two fragments identified were associated with possible virulence factors. One fragment was identical to irsA of Salmonella serovar Typhimurium ATCC 14028, which is suggested to be involved in macrophage survival. The other fragment was homologous to HldD, an Escherichia coli O157:H7 lipopolysaccharide

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17

Liu, Benchao, Junru Zhao, Hui Chen, et al. "RH2Fusion: A universal tool for precise DNA fragment assembly." International Journal of Biological Macromolecules 288 (February 2025): 138788. https://doi.org/10.1016/j.ijbiomac.2024.138788.

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18

Xu, Baomin, Jin Gao, and Chunyan Li. "An efficient algorithm for DNA fragment assembly in MapReduce." Biochemical and Biophysical Research Communications 426, no. 3 (2012): 395–98. http://dx.doi.org/10.1016/j.bbrc.2012.08.101.

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19

Prjibelski, A. D., I. Vasilinetc, A. Bankevich, et al. "ExSPAnder: a universal repeat resolver for DNA fragment assembly." Bioinformatics 30, no. 12 (2014): i293—i301. http://dx.doi.org/10.1093/bioinformatics/btu266.

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20

Zherenkova, L. V., P. V. Komarov, P. G. Khalatur, and A. R. Khokhlov. "Nanowire self-assembly on a DNA fragment: Computer simulation." Doklady Physical Chemistry 421, no. 2 (2008): 207–10. http://dx.doi.org/10.1134/s0012501608080046.

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21

Nebro, A. J., G. Luque, F. Luna, and E. Alba. "DNA fragment assembly using a grid-based genetic algorithm." Computers & Operations Research 35, no. 9 (2008): 2776–90. http://dx.doi.org/10.1016/j.cor.2006.12.011.

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22

Vidal, Pablo, and Ana Olivera. "Solving the DNA fragment assembly problem with a parallel discrete firefly algorithm implemented on GPU." Computer Science and Information Systems 15, no. 2 (2018): 273–93. http://dx.doi.org/10.2298/csis170510009v.

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The Deoxyribonucleic Acid Fragment Assembly Problem (DNA-FAP) consists in reconstructing a DNA chain from a set of fragments taken randomly. This problem represents an important step in the genome project. Several authors are proposed different approaches to solve the DNA-FAP. In particular, nature-inspired algorithms have been used for its resolution. Even they were obtaining good results; its computational time associated is high. The bio-inspired algorithms are iterative search processes that can explore and exploit efficiently the solution space. Firefly Algorithm is one of the recent evol

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23

Padovani de Souza, Kleber, João Carlos Setubal, André Carlos Ponce de Leon F. de Carvalho, Guilherme Oliveira, Annie Chateau, and Ronnie Alves. "Machine learning meets genome assembly." Briefings in Bioinformatics 20, no. 6 (2018): 2116–29. http://dx.doi.org/10.1093/bib/bby072.

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Abstract Motivation: With the recent advances in DNA sequencing technologies, the study of the genetic composition of living organisms has become more accessible for researchers. Several advances have been achieved because of it, especially in the health sciences. However, many challenges which emerge from the complexity of sequencing projects remain unsolved. Among them is the task of assembling DNA fragments from previously unsequenced organisms, which is classified as an NP-hard (nondeterministic polynomial time hard) problem, for which no efficient computational solution with reasonable ex

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24

Matsuno, Kumiko, Maya Kumano, Yumiko Kubota, Yoshitami Hashimoto та Haruhiko Takisawa. "The N-Terminal Noncatalytic Region of Xenopus RecQ4 Is Required for Chromatin Binding of DNA Polymerase α in the Initiation of DNA Replication". Molecular and Cellular Biology 26, № 13 (2006): 4843–52. http://dx.doi.org/10.1128/mcb.02267-05.

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ABSTRACT Recruitment of DNA polymerases onto replication origins is a crucial step in the assembly of eukaryotic replication machinery. A previous study in budding yeast suggests that Dpb11 controls the recruitment of DNA polymerases α and ε onto the origins. Sld2 is an essential replication protein that interacts with Dpb11, but no metazoan homolog has yet been identified. We isolated Xenopus RecQ4 as a candidate Sld2 homolog. RecQ4 is a member of the metazoan RecQ helicase family, and its N-terminal region shows sequence similarity with Sld2. In Xenopus egg extracts, RecQ4 is essential for t

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25

Guo, Yujing, Guang Cai, Huiying Li, et al. "A CRISPR-Cas9-Mediated Large-Fragment Assembly Method for Cloning Genomes and Biosynthetic Gene Cluster." Microorganisms 12, no. 7 (2024): 1462. http://dx.doi.org/10.3390/microorganisms12071462.

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The ability to clone large DNA fragments from genomes is valuable for both basic and applied research, such as the construction of synthetic genomes, and the expression of biosynthetic gene clusters (BGCs) for natural product discovery. Here, we report a fast and efficient platform for the direct capture of genome DNAs, by combining CRISPR and Gibson assembly. We demonstrate this method with the ability of cloning large DNA fragments ranging from 30 to 77 kb from various host genomes, achieving a near 100% cloning fidelity for DNA fragments below 50 kb. We next demonstrate this method by the c

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Ibrahim, Abdul-Wahab, Baidaa Atya, Amaal Khdum, and Enas Hessian. "Using Simulated Annealing to solve the DNA Fragment Assembly Problem." Journal of Al-Rafidain University College For Sciences ( Print ISSN: 1681-6870 ,Online ISSN: 2790-2293 ), no. 1 (October 23, 2021): 25–34. http://dx.doi.org/10.55562/jrucs.v26i1.420.

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Different ways have used to solve the problem of simple division of DNA and the results have been obtained by the researchers varied between good results and the other did not reach the desired results. In this research, has been proposed to use the formulation of a new method to change any form by use of heating, which relies on the principle of physics idea was to bring the heat for metals and thus gradually change shape to form the required start as high a temperature and decreasing gradually to get the required form of the metal. Applying the same principle we enable for getting simple sol

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Mallén-Fullerton, Guillermo, J. Quiroz-Ibarra, Antonio Miranda, and Guillermo Fernández-Anaya. "Modified Classical Graph Algorithms for the DNA Fragment Assembly Problem." Algorithms 8, no. 3 (2015): 754–73. http://dx.doi.org/10.3390/a8030754.

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Fang, Shu-Cherng, Yong Wang, and Jie Zhong. "A Genetic Algorithm Approach to Solving DNA Fragment Assembly Problem." Journal of Computational and Theoretical Nanoscience 2, no. 4 (2005): 499–505. http://dx.doi.org/10.1166/jctn.2005.004.

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Fang, Shu-Cherng, Yong Wang, and Jie Zhong. "A Genetic Algorithm Approach to Solving DNA Fragment Assembly Problem." Journal of Computational and Theoretical Nanoscience 2, no. 4 (2005): 499–505. http://dx.doi.org/10.1166/jctn.2005.2974.

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30

Gupta, Yash Munnalal, Kittisak Buddhachat, Surin Peyachoknagul, and Somjit Homchan. "Novel DNA Barcode Sequence Discovery from Transcriptome of Acheta domesticus: A Partial Mitochondrial DNA." Materials Science Forum 967 (August 2019): 59–64. http://dx.doi.org/10.4028/www.scientific.net/msf.967.59.

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The potential of mitochondrial DNA (mtDNA) genes are well-known for species identification and to establish a phylogenetic relationship. The De-novo transcriptome assembly of Acheta domesticus commonly known as house cricket, is provides important segments of DNA fragments from mitochondrial DNA due to higher abundance of its mRNA. When the reference sequence with gene annotation is absent for assembling and aligning desire gene sequences, like in the present case, the most similar sequence is obtained from online insect mitochondrial genome database to find mitochondrial DNA conserved domains

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Fedorov, A. V., Ya M. Krasnov, E. A. Naryshkina, et al. "Hybrid Assembly of Complete Genomes of <I>Yersinia pestis</I> Strains." Problems of Particularly Dangerous Infections, no. 1 (April 4, 2024): 176–81. http://dx.doi.org/10.21055/0370-1069-2024-1-176-181.

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The aim of the study was to assemble full-length nucleotide sequences of the chromosome and plasmids for 13 Yersinia pestis strains from 11 natural plague foci located in the Russian Federation, using data from two sequencing technologies.Materials and methods. Y. pestis strains were grown on Hottinger’s agar (pH 7.2) at 37 °C. DNA was isolated using phenol-chloroform extraction. For the MinIon genetic analyzer (Oxford Nanopore), DNA fragments were prepared by ligation according to a modified protocol. For the Ion S5 genetic analyzer (IonTorrent), sample preparation was carried out according t

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Shiina, Masaaki, Keisuke Hamada, Taiko Inoue-Bungo та ін. "Crystallization of the Ets1–Runx1–CBFβ–DNA complex formed on the TCRα gene enhancer". Acta Crystallographica Section F Structural Biology Communications 70, № 10 (2014): 1380–84. http://dx.doi.org/10.1107/s2053230x14018470.

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Gene transcription is regulated in part through the assembly of multiple transcription factors (TFs) on gene enhancers. To enable examination of the mechanism underlying the formation of these complexes and their response to a phosphorylation signal, two kinds of higher-order TF–DNA assemblies were crystallized composed of an unmodified or phosphorylated Ets1 fragment, a Runx1(L94K) fragment and a CBFβ fragment on the T-cell receptor (TCR) α gene enhancer. Within these complexes, the Ets1 and Runx1 fragments contain intrinsically disordered regulatory regions as well as their DNA-binding domai

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Abdel-Basset, Mohamed, Reda Mohamed, Karam M. Sallam, Ripon K. Chakrabortty, and Michael J. Ryan. "An Efficient-Assembler Whale Optimization Algorithm for DNA Fragment Assembly Problem: Analysis and Validations." IEEE Access 8 (2020): 222144–67. http://dx.doi.org/10.1109/access.2020.3044857.

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34

Indumathy, R. "Nature Inspired Algorithms To Solve DNA Fragment Assembly Problem: A Survey." International Journal on Bioinformatics & Biosciences 2, no. 2 (2012): 45–50. http://dx.doi.org/10.5121/ijbb.2012.2205.

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35

Huang, Ko-Wei, Jui-Le Chen, Chu-Sing Yang, and Chun-Wei Tsai. "A memetic gravitation search algorithm for solving DNA fragment assembly problems." Journal of Intelligent & Fuzzy Systems 30, no. 4 (2016): 2245–55. http://dx.doi.org/10.3233/ifs-151994.

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Bartolami, Eline, Yannick Bessin, Nadir Bettache, et al. "Multivalent DNA recognition by self-assembled clusters: deciphering structural effects by fragments screening and evaluation as siRNA vectors." Organic & Biomolecular Chemistry 13, no. 36 (2015): 9427–38. http://dx.doi.org/10.1039/c5ob01404b.

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37

Campbell, Stephen, and Alan Rein. "In Vitro Assembly Properties of Human Immunodeficiency Virus Type 1 Gag Protein Lacking the p6 Domain." Journal of Virology 73, no. 3 (1999): 2270–79. http://dx.doi.org/10.1128/jvi.73.3.2270-2279.1999.

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ABSTRACT Human immunodeficiency virus type 1 (HIV-1) normally assembles into particles of 100 to 120 nm in diameter by budding through the plasma membrane of the cell. The Gag polyprotein is the only viral protein that is required for the formation of these particles. We have used an in vitro assembly system to examine the assembly properties of purified, recombinant HIV-1 Gag protein and of Gag missing the C-terminal p6 domain (Gag Δp6). This system was used previously to show that the CA-NC fragment of HIV-1 Gag assembled into cylindrical particles. We now report that both HIV-1 Gag and Gag

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Kaneko, Shinya, Hiromi Fukushima, Misako Nakahama, et al. "DNA synthesis by fragment assembly using extra-cellular DNA delivered by artificial controlled horizontal transfer." Journal of Biochemistry 163, no. 4 (2017): 305–12. http://dx.doi.org/10.1093/jb/mvx085.

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39

Rajagopal, Indumathy, and Uma Sankareswaran. "An Adaptive Particle Swarm Optimization Algorithm for Solving DNA Fragment Assembly Problem." Current Bioinformatics 10, no. 1 (2015): 97–105. http://dx.doi.org/10.2174/1574893609666140301001642.

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Uzma and Zahid Halim. "Optimizing the DNA fragment assembly using metaheuristic-based overlap layout consensus approach." Applied Soft Computing 92 (July 2020): 106256. http://dx.doi.org/10.1016/j.asoc.2020.106256.

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Allaoui, Mohcin, Belaïd Ahiod, and Mohamed El Yafrani. "A hybrid crow search algorithm for solving the DNA fragment assembly problem." Expert Systems with Applications 102 (July 2018): 44–56. http://dx.doi.org/10.1016/j.eswa.2018.02.018.

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Minetti, Gabriela, Enrique Alba, and Gabriel Luque. "Seeding strategies and recombination operators for solving the DNA fragment assembly problem." Information Processing Letters 108, no. 3 (2008): 94–100. http://dx.doi.org/10.1016/j.ipl.2008.04.005.

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Amundsen, Susan K., Andrew F. Taylor, and Gerald R. Smith. "A Domain of RecC Required for Assembly of the Regulatory RecD Subunit Into the Escherichia coli RecBCD Holoenzyme." Genetics 161, no. 2 (2002): 483–92. http://dx.doi.org/10.1093/genetics/161.2.483.

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Abstract The heterotrimeric RecBCD enzyme of Escherichia coli is required for the major pathway of double-strand DNA break repair and genetic exchange. Assembled as a heterotrimer, the enzyme has potent nuclease and helicase activity. Analysis of recC nonsense and deletion mutations revealed that the C terminus of RecC is required for assembly of the RecD subunit into RecBCD holoenzyme but not for recombination proficiency; the phenotype of these mutations mimics that of recD deletion mutations. Partial proteolysis of purified RecC polypeptide yielded a C-terminal fragment that corresponds to

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Zhang, Wei, and Michael J. Imperiale. "Requirement of the Adenovirus IVa2 Protein for Virus Assembly." Journal of Virology 77, no. 6 (2003): 3586–94. http://dx.doi.org/10.1128/jvi.77.6.3586-3594.2003.

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ABSTRACT The adenovirus L1 52/55-kDa protein is required for viral DNA packaging and interacts with the viral IVa2 protein, which binds to the viral packaging sequence. Previous reports suggest that the IVa2 protein plays a role in viral DNA packaging and that this function of the IVa2 protein is serotype specific. To further examine the function of the IVa2 protein in viral DNA packaging, a mutant virus that does not express the IVa2 protein was constructed by introducing two stop codons at the beginning of the IVa2 open reading frame in a full-length bacterial clone of adenovirus type 5. The

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45

Thompson, Robert E., Frédéric Collin, Anthony Maxwell, Katrina A. Jolliffe, and Richard J. Payne. "Synthesis of full length and truncated microcin B17 analogues as DNA gyrase poisons." Org. Biomol. Chem. 12, no. 10 (2014): 1570–78. http://dx.doi.org/10.1039/c3ob42516a.

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Using a combination of solid-phase peptide synthesis and fragment assembly strategies a library of full-length and truncated analogues of the antibacterial post-translationally modified peptide microcin B17 have been synthesised. Both antibacterial and DNA gyrase poisoning activities are also described for the synthetic analogues.

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Penny, Christian, Thierry Nadalig, Malek Alioua, Christelle Gruffaz, Stéphane Vuilleumier, and Françoise Bringel. "Coupling of Denaturing High-Performance Liquid Chromatography and Terminal Restriction Fragment Length Polymorphism with Precise Fragment Sizing for Microbial Community Profiling and Characterization." Applied and Environmental Microbiology 76, no. 3 (2009): 648–51. http://dx.doi.org/10.1128/aem.01556-09.

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ABSTRACT Terminal restriction fragment length polymorphism (T-RFLP) is used to monitor the structural diversity of complex microbial communities in terms of richness, relative abundance, and distribution of the major subpopulations and individual members. However, discrepancies of several nucleotides between expected and experimentally observed lengths of terminal restriction fragments (T-RFs), together with the difficulty of obtaining DNA sequence information from T-RFLP profiling, often prevent accurate phylogenetic characterization of the microbial community of interest. In this study, T-RF

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Ben Ali, Abdelkamel, Gabriel Luque, Enrique Alba, and Kamal E. Melkemi. "An improved problem aware local search algorithm for the DNA fragment assembly problem." Soft Computing 21, no. 7 (2015): 1709–20. http://dx.doi.org/10.1007/s00500-015-1875-2.

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Huang, Ko-Wei, Jui-Le Chen, Chu-Sing Yang, and Chun-Wei Tsai. "A memetic particle swarm optimization algorithm for solving the DNA fragment assembly problem." Neural Computing and Applications 26, no. 3 (2014): 495–506. http://dx.doi.org/10.1007/s00521-014-1659-0.

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Kuśmirek, Wiktor, Wiktor Franus, and Robert Nowak. "Linking De Novo Assembly Results with Long DNA Reads Using the dnaasm-link Application." BioMed Research International 2019 (April 11, 2019): 1–10. http://dx.doi.org/10.1155/2019/7847064.

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Currently, third-generation sequencing techniques, which make it possible to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities for combining data from next-generation and third-generation sequencing. Herein, we present a new application called dnaasm-link for linking contigs, the result of de novo assembly of second-generation sequencing data, with long DNA reads. Our tool includes an integrated module to fill gaps with a suitable fragment of an appropriate long DNA read, which improves the con

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Wang, Lei, Xing Dai, Yujian Feng, et al. "Dual Catalytic Hairpin Assembly-Based Automatic Molecule Machine for Amplified Detection of Auxin Response Factor-Targeted MicroRNA-160." Molecules 26, no. 21 (2021): 6432. http://dx.doi.org/10.3390/molecules26216432.

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Abstract:

MicroRNA160 plays a crucial role in plant development by negatively regulating the auxin response factors (ARFs). In this manuscript, we design an automatic molecule machine (AMM) based on the dual catalytic hairpin assembly (D-CHA) strategy for the signal amplification detection of miRNA160. The detection system contains four hairpin-shaped DNA probes (HP1, HP2, HP3, and HP4). For HP1, the loop is designed to be complementary to miRNA160. A fragment of DNA with the same sequences as miRNA160 is separated into two pieces that are connected at the 3′ end of HP2 and 5′ end of HP3, respectively.

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