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For: Brázda V, Kolomazník J, Lýsek J, Hároníková L, Coufal J, Št'astný J. Palindrome analyser - A new web-based server for predicting and evaluating inverted repeats in nucleotide sequences. Biochem Biophys Res Commun 2016;478:1739-45. [PMID: 27603574 DOI: 10.1016/j.bbrc.2016.09.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 09/02/2016] [Indexed: 10/21/2022]
Number Cited by Other Article(s)
1
Bartas M, Brázda V, Pečinka P. Special Issue "Bioinformatics of Unusual DNA and RNA Structures". Int J Mol Sci 2024;25:5226. [PMID: 38791265 PMCID: PMC11121459 DOI: 10.3390/ijms25105226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 04/29/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024]  Open
2
Yang CC, Wang ZY, Cheng CM. Insights into Superinfection Immunity Regulation of Xanthomonas axonopodis Filamentous Bacteriophage cf. Curr Microbiol 2023;81:42. [PMID: 38112972 DOI: 10.1007/s00284-023-03539-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 10/26/2023] [Indexed: 12/21/2023]
3
Song K, Brochu HN, Zhang Q, Williams JD, Iyer LK. An In Silico Analysis of PCR-Based Monkeypox Virus Detection Assays: A Case Study for Ongoing Clinical Surveillance. Viruses 2023;15:2327. [PMID: 38140568 PMCID: PMC10747849 DOI: 10.3390/v15122327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023]  Open
4
Yella VR, Vanaja A. Computational analysis on the dissemination of non-B DNA structural motifs in promoter regions of 1180 cellular genomes. Biochimie 2023;214:101-111. [PMID: 37311475 DOI: 10.1016/j.biochi.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 05/05/2023] [Accepted: 06/05/2023] [Indexed: 06/15/2023]
5
Porubiaková O, Havlík J, Indu, Šedý M, Přepechalová V, Bartas M, Bidula S, Šťastný J, Fojta M, Brázda V. Variability of Inverted Repeats in All Available Genomes of Bacteria. Microbiol Spectr 2023;11:e0164823. [PMID: 37358458 PMCID: PMC10434271 DOI: 10.1128/spectrum.01648-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/03/2023] [Indexed: 06/27/2023]  Open
6
Getz LJ, Brown JM, Sobot L, Chow A, Mahendrarajah J, Thomas N. Attenuation of a DNA cruciform by a conserved regulator directs T3SS1 mediated virulence in Vibrio parahaemolyticus. Nucleic Acids Res 2023;51:6156-6171. [PMID: 37158250 PMCID: PMC10325908 DOI: 10.1093/nar/gkad370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/23/2023] [Accepted: 04/27/2023] [Indexed: 05/10/2023]  Open
7
Kwok ACM, Leung SK, Wong JTY. DNA:RNA Hybrids Are Major Dinoflagellate Minicircle Molecular Types. Int J Mol Sci 2023;24:ijms24119651. [PMID: 37298602 DOI: 10.3390/ijms24119651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023]  Open
8
Bastos CAC, Afreixo V, Rodrigues JMOS, Pinho AJ. Concentration of inverted repeats along human DNA. J Integr Bioinform 2023;20:jib-2022-0052. [PMID: 37486620 PMCID: PMC10561070 DOI: 10.1515/jib-2022-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/27/2023] [Indexed: 07/25/2023]  Open
9
Valková N, Kratochvilová L, Martinková L, Brázda V. Dual mode of IFI16 binding to supercoiled and linear DNA: A closer insight. Biochem Biophys Res Commun 2023;667:89-94. [PMID: 37209567 DOI: 10.1016/j.bbrc.2023.05.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 05/14/2023] [Indexed: 05/22/2023]
10
Genomic Analysis of Non-B Nucleic Acids Structures in SARS-CoV-2: Potential Key Roles for These Structures in Mutability, Translation, and Replication? Genes (Basel) 2023;14:genes14010157. [PMID: 36672896 PMCID: PMC9859294 DOI: 10.3390/genes14010157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/01/2023] [Accepted: 01/04/2023] [Indexed: 01/09/2023]  Open
11
Dobrovolná M, Brázda V, Warner EF, Bidula S. Inverted repeats in the monkeypox virus genome are hot spots for mutation. J Med Virol 2023;95:e28322. [PMID: 36400742 PMCID: PMC10100261 DOI: 10.1002/jmv.28322] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/21/2022]
12
Goswami P, Šislerová L, Dobrovolná M, Havlík J, Šťastný J, Brázda V. Interaction of C-terminal p53 isoforms depends strongly upon DNA sequence and topology. Biochimie 2022;208:93-99. [PMID: 36549455 DOI: 10.1016/j.biochi.2022.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
13
Shi X, Teng H, Sun Z. An updated overview of experimental and computational approaches to identify non-canonical DNA/RNA structures with emphasis on G-quadruplexes and R-loops. Brief Bioinform 2022;23:bbac441. [PMID: 36208174 PMCID: PMC9677470 DOI: 10.1093/bib/bbac441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/22/2022] [Accepted: 09/13/2022] [Indexed: 12/14/2022]  Open
14
Dobrovolná M, Bohálová N, Peška V, Wang J, Luo Y, Bartas M, Volná A, Mergny JL, Brázda V. The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences-Implications for Evolution and Biological Regulation. Int J Mol Sci 2022;23:8482. [PMID: 35955617 PMCID: PMC9369095 DOI: 10.3390/ijms23158482] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 11/20/2022]  Open
15
Rakpenthai A, Apodiakou A, Whitcomb SJ, Hoefgen R. In silico analysis of cis-elements and identification of transcription factors putatively involved in the regulation of the OAS cluster genes SDI1 and SDI2. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022;110:1286-1304. [PMID: 35315155 DOI: 10.1111/tpj.15735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 02/09/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
16
Bowater RP, Bohálová N, Brázda V. Interaction of Proteins with Inverted Repeats and Cruciform Structures in Nucleic Acids. Int J Mol Sci 2022;23:ijms23116171. [PMID: 35682854 PMCID: PMC9180970 DOI: 10.3390/ijms23116171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 01/27/2023]  Open
17
Pánek T, Barcytė D, Treitli SC, Záhonová K, Sokol M, Ševčíková T, Zadrobílková E, Jaške K, Yubuki N, Čepička I, Eliáš M. A new lineage of non-photosynthetic green algae with extreme organellar genomes. BMC Biol 2022;20:66. [PMID: 35296310 PMCID: PMC8928634 DOI: 10.1186/s12915-022-01263-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/22/2022] [Indexed: 12/27/2022]  Open
18
Víglaský V. Hidden Information Revealed Using the Orthogonal System of Nucleic Acids. Int J Mol Sci 2022;23:ijms23031804. [PMID: 35163723 PMCID: PMC8836696 DOI: 10.3390/ijms23031804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/31/2022] [Accepted: 02/02/2022] [Indexed: 11/25/2022]  Open
19
Skorupski J. Characterisation of the Complete Mitochondrial Genome of Critically Endangered Mustela lutreola (Carnivora: Mustelidae) and Its Phylogenetic and Conservation Implications. Genes (Basel) 2022;13:genes13010125. [PMID: 35052465 PMCID: PMC8774856 DOI: 10.3390/genes13010125] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/28/2021] [Accepted: 01/06/2022] [Indexed: 02/07/2023]  Open
20
Bacolla A, Tainer JA. Robust Computational Approaches to Defining Insights on the Interface of DNA Repair with Replication and Transcription in Cancer. Methods Mol Biol 2022;2444:1-13. [PMID: 35290628 PMCID: PMC9377048 DOI: 10.1007/978-1-0716-2063-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
21
Inverted repeats in coronavirus SARS-CoV-2 genome manifest the evolution events. J Theor Biol 2021;530:110885. [PMID: 34478743 PMCID: PMC8406619 DOI: 10.1016/j.jtbi.2021.110885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/13/2021] [Accepted: 08/25/2021] [Indexed: 11/24/2022]
22
The minicircular and extremely heteroplasmic mitogenome of the holoparasitic plant Rhopalocnemis phalloides. Curr Biol 2021;32:470-479.e5. [PMID: 34906352 DOI: 10.1016/j.cub.2021.11.053] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/25/2021] [Accepted: 11/22/2021] [Indexed: 12/14/2022]
23
R-Loop Tracker: Web Access-Based Tool for R-Loop Detection and Analysis in Genomic DNA Sequences. Int J Mol Sci 2021;22:ijms222312857. [PMID: 34884661 PMCID: PMC8657672 DOI: 10.3390/ijms222312857] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/19/2021] [Accepted: 11/25/2021] [Indexed: 12/02/2022]  Open
24
Brázda V, Bohálová N, Bowater RP. New telomere to telomere assembly of human chromosome 8 reveals a previous underestimation of G-quadruplex forming sequences and inverted repeats. Gene 2021;810:146058. [PMID: 34737002 DOI: 10.1016/j.gene.2021.146058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/14/2021] [Accepted: 10/29/2021] [Indexed: 11/04/2022]
25
Emrich-Mills TZ, Yates G, Barrett J, Girr P, Grouneva I, Lau CS, Walker CE, Kwok TK, Davey JW, Johnson MP, Mackinder LCM. A recombineering pipeline to clone large and complex genes in Chlamydomonas. THE PLANT CELL 2021;33:1161-1181. [PMID: 33723601 PMCID: PMC8633747 DOI: 10.1093/plcell/koab024] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 01/18/2021] [Indexed: 05/10/2023]
26
Brázda V, Bartas M, Bowater RP. Evolution of Diverse Strategies for Promoter Regulation. Trends Genet 2021;37:730-744. [PMID: 33931265 DOI: 10.1016/j.tig.2021.04.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 12/15/2022]
27
Goswami P, Bartas M, Lexa M, Bohálová N, Volná A, Červeň J, Červeňová V, Pečinka P, Špunda V, Fojta M, Brázda V. SARS-CoV-2 hot-spot mutations are significantly enriched within inverted repeats and CpG island loci. Brief Bioinform 2021;22:1338-1345. [PMID: 33341900 PMCID: PMC7799342 DOI: 10.1093/bib/bbaa385] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/16/2020] [Accepted: 11/27/2020] [Indexed: 12/18/2022]  Open
28
Bartas M, Goswami P, Lexa M, Červeň J, Volná A, Fojta M, Brázda V, Pečinka P. Letter to the Editor: Significant mutation enrichment in inverted repeat sites of new SARS-CoV-2 strains. Brief Bioinform 2021;22:6219140. [PMID: 33837760 PMCID: PMC8083281 DOI: 10.1093/bib/bbab129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/16/2021] [Accepted: 03/19/2021] [Indexed: 01/08/2023]  Open
29
Tracing dsDNA Virus-Host Coevolution through Correlation of Their G-Quadruplex-Forming Sequences. Int J Mol Sci 2021;22:ijms22073433. [PMID: 33810462 PMCID: PMC8036883 DOI: 10.3390/ijms22073433] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/17/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022]  Open
30
Zell J, Rota Sperti F, Britton S, Monchaud D. DNA folds threaten genetic stability and can be leveraged for chemotherapy. RSC Chem Biol 2021;2:47-76. [PMID: 35340894 PMCID: PMC8885165 DOI: 10.1039/d0cb00151a] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/20/2020] [Indexed: 12/22/2022]  Open
31
Karageorgiou C, Tarrío R, Rodríguez-Trelles F. The Cyclically Seasonal Drosophila subobscura Inversion O7 Originated From Fragile Genomic Sites and Relocated Immunity and Metabolic Genes. Front Genet 2020;11:565836. [PMID: 33193649 PMCID: PMC7584159 DOI: 10.3389/fgene.2020.565836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/09/2020] [Indexed: 11/28/2022]  Open
32
Brázda V, Luo Y, Bartas M, Kaura P, Porubiaková O, Šťastný J, Pečinka P, Verga D, Da Cunha V, Takahashi TS, Forterre P, Myllykallio H, Fojta M, Mergny JL. G-Quadruplexes in the Archaea Domain. Biomolecules 2020;10:biom10091349. [PMID: 32967357 PMCID: PMC7565180 DOI: 10.3390/biom10091349] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 11/26/2022]  Open
33
An J, Zheng W, Liang J, Xi Q, Chen R, Jia J, Lu X, Jakovlić I. Disrupted architecture and fast evolution of the mitochondrial genome of Argeia pugettensis (Isopoda): implications for speciation and fitness. BMC Genomics 2020;21:607. [PMID: 32883208 PMCID: PMC7469299 DOI: 10.1186/s12864-020-07021-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/24/2020] [Indexed: 11/24/2022]  Open
34
Liu X, Wu X, Tan H, Xie B, Deng Y. Large inverted repeats identified by intra-specific comparison of mitochondrial genomes provide insights into the evolution of Agrocybe aegerita. Comput Struct Biotechnol J 2020;18:2424-2437. [PMID: 33005305 PMCID: PMC7508693 DOI: 10.1016/j.csbj.2020.08.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 11/29/2022]  Open
35
Bartas M, Brázda V, Bohálová N, Cantara A, Volná A, Stachurová T, Malachová K, Jagelská EB, Porubiaková O, Červeň J, Pečinka P. In-Depth Bioinformatic Analyses of Nidovirales Including Human SARS-CoV-2, SARS-CoV, MERS-CoV Viruses Suggest Important Roles of Non-canonical Nucleic Acid Structures in Their Lifecycles. Front Microbiol 2020;11:1583. [PMID: 32719673 PMCID: PMC7347907 DOI: 10.3389/fmicb.2020.01583] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022]  Open
36
Global analysis of inverted repeat sequences in human gene promoters reveals their non-random distribution and association with specific biological pathways. Genomics 2020;112:2772-2777. [DOI: 10.1016/j.ygeno.2020.03.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/02/2020] [Accepted: 03/20/2020] [Indexed: 12/11/2022]
37
Dupeyron M, Baril T, Bass C, Hayward A. Phylogenetic analysis of the Tc1/mariner superfamily reveals the unexplored diversity of pogo-like elements. Mob DNA 2020;11:21. [PMID: 32612713 PMCID: PMC7325037 DOI: 10.1186/s13100-020-00212-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/08/2020] [Indexed: 01/18/2023]  Open
38
Zhang R, Ge F, Li H, Chen Y, Zhao Y, Gao Y, Liu Z, Yang L. PCIR: a database of Plant Chloroplast Inverted Repeats. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020;2019:5611292. [PMID: 31696928 PMCID: PMC6835207 DOI: 10.1093/database/baz127] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/26/2019] [Accepted: 10/07/2019] [Indexed: 01/06/2023]
39
The Rich World of p53 DNA Binding Targets: The Role of DNA Structure. Int J Mol Sci 2019;20:ijms20225605. [PMID: 31717504 PMCID: PMC6888028 DOI: 10.3390/ijms20225605] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/29/2019] [Accepted: 11/08/2019] [Indexed: 12/14/2022]  Open
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Čutová M, Manta J, Porubiaková O, Kaura P, Šťastný J, Jagelská EB, Goswami P, Bartas M, Brázda V. Divergent distributions of inverted repeats and G-quadruplex forming sequences in Saccharomyces cerevisiae. Genomics 2019;112:1897-1901. [PMID: 31706022 DOI: 10.1016/j.ygeno.2019.11.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/13/2019] [Accepted: 11/01/2019] [Indexed: 12/17/2022]
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Brázda V, Kolomazník J, Lýsek J, Bartas M, Fojta M, Šťastný J, Mergny JL. G4Hunter web application: a web server for G-quadruplex prediction. Bioinformatics 2019;35:3493-3495. [PMID: 30721922 PMCID: PMC6748775 DOI: 10.1093/bioinformatics/btz087] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 01/08/2019] [Accepted: 02/04/2019] [Indexed: 12/26/2022]  Open
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Bartas M, Čutová M, Brázda V, Kaura P, Šťastný J, Kolomazník J, Coufal J, Goswami P, Červeň J, Pečinka P. The Presence and Localization of G-Quadruplex Forming Sequences in the Domain of Bacteria. Molecules 2019;24:molecules24091711. [PMID: 31052562 PMCID: PMC6539912 DOI: 10.3390/molecules24091711] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 04/30/2019] [Accepted: 05/01/2019] [Indexed: 01/09/2023]  Open
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Dupeyron M, Singh KS, Bass C, Hayward A. Evolution of Mutator transposable elements across eukaryotic diversity. Mob DNA 2019;10:12. [PMID: 30988700 PMCID: PMC6446971 DOI: 10.1186/s13100-019-0153-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 03/01/2019] [Indexed: 11/15/2022]  Open
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Bartas M, Bažantová P, Brázda V, Liao JC, Červeň J, Pečinka P. Identification of Distinct Amino Acid Composition of Human Cruciform Binding Proteins. Mol Biol 2019. [DOI: 10.1134/s0026893319010023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Cechová J, Lýsek J, Bartas M, Brázda V. Complex analyses of inverted repeats in mitochondrial genomes revealed their importance and variability. Bioinformatics 2019;34:1081-1085. [PMID: 29126205 PMCID: PMC6030915 DOI: 10.1093/bioinformatics/btx729] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/07/2017] [Indexed: 01/08/2023]  Open
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Zou H, Jakovlić I, Zhang D, Chen R, Mahboob S, Al-Ghanim KA, Al-Misned F, Li WX, Wang GT. The complete mitochondrial genome of Cymothoa indica has a highly rearranged gene order and clusters at the very base of the Isopoda clade. PLoS One 2018;13:e0203089. [PMID: 30180209 PMCID: PMC6122833 DOI: 10.1371/journal.pone.0203089] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/14/2018] [Indexed: 11/18/2022]  Open
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Mandal S, Selvam S, Cui Y, Hoque ME, Mao H. Mechanical Cooperativity in DNA Cruciform Structures. Chemphyschem 2018;19:2627-2634. [PMID: 29992736 DOI: 10.1002/cphc.201800480] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Indexed: 01/20/2023]
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Complex Analyses of Short Inverted Repeats in All Sequenced Chloroplast DNAs. BIOMED RESEARCH INTERNATIONAL 2018;2018:1097018. [PMID: 30140690 PMCID: PMC6081594 DOI: 10.1155/2018/1097018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 06/19/2018] [Accepted: 07/12/2018] [Indexed: 01/14/2023]
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Čechová J, Coufal J, Jagelská EB, Fojta M, Brázda V. p73, like its p53 homolog, shows preference for inverted repeats forming cruciforms. PLoS One 2018;13:e0195835. [PMID: 29668749 PMCID: PMC5905954 DOI: 10.1371/journal.pone.0195835] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/01/2018] [Indexed: 12/12/2022]  Open
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Miura O, Ogake T, Ohyama T. Requirement or exclusion of inverted repeat sequences with cruciform-forming potential in Escherichia coli revealed by genome-wide analyses. Curr Genet 2018;64:945-958. [PMID: 29484452 PMCID: PMC6060812 DOI: 10.1007/s00294-018-0815-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/16/2018] [Accepted: 02/19/2018] [Indexed: 12/31/2022]
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