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Volume 20   Issue 2   Year 2025
References

  1. Schnable P.S., Ware D., Fulton R.S., Stein J.C., Wei F., Pasternak S., Liang C., Zhang J., Fulton L., Graves T.A., et al. The B73 maize genome: complexity, diversity, and dynamics. Science. 2009;326:1112–1115. doi: 10.1126/science.1178534
  2. de Koning A.P., Gu W., Castoe T.A., Batzer M.A., Pollock D.D. Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet. 2011;7. Article No. e1002384. doi: 10.1371/journal.pgen
  3. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W. et al. Initial sequencing and analysis of the human genome. Nature. 2001;409:860–921. doi: 10.1038/35057062
  4. Orgel L.E., Crick F.H. Selfish DNA: the ultimate parasite. Nature. 1980;284:604–607. doi: 10.1038/284604a0
  5. Hannan A.J. Tandem repeat polymorphisms: mediators of genetic plasticity, modulators of biological diversity and dynamic sources of disease susceptibility. Adv. Exp. Med. Biol. 2012;769:1–9. doi: 10.1007/978-1-4614-5434-2_1
  6. Charlesworth B., Sniegowski P., Stephan W. The evolutionary dynamics of repetitive DNA in eukaryotes. Nature. 1994;371:215–220. doi: 10.1038/371215a0
  7. Davidson E.H., Britten R.J. Regulation of gene expression: possible role of repetitive sequences. Science. 1979;204:1052–1059. doi: 10.1126/science.45154
  8. Mirkin S.M. Expandable DNA repeats and human disease. Nature. 2007;447:932–940. doi: 10.1038/nature05977
  9. Gymrek M., Willems T., Guilmatre A. Abundant contribution of short tandem repeats to gene expression variation in humans. Nat. Genet. 2016;48:22–29. doi: 10.1038/ng.3461
  10. Hannan A.J. Tandem repeats mediating genetic plasticity in health and disease. Nat. Rev. Genet. 2018;19:286–298. doi: 10.1038/nrg.2017.115
  11. Vollger M.R., Dishuck P.C., Sorensen M., Welch A.E., Dang V., Dougherty M.L., Graves-Lindsay T.A., Wilson R.K., Chaisson M.J.P., Eichler E.E. Long-read sequence and assembly of segmental duplications. Nat. Methods. 2019;16:88–94. doi: 10.1038/s41592-018-0236-3
  12. Nurk S., Koren S., Rhie A., Rautiainen M., Bzikadze A.V., Mikheenko A., Vollger M.R., Altemose N., Uralsky L., Gershman A., et al. The complete sequence of a human genome. Science. 2022;376:44–53. doi: 10.1126/science.abj6987
  13. Feng C., Dai M., Liu Y., Chen M. Sequence repetitiveness quantification and de novo repeat detection by weighted k-mer coverage. Brief Bioinform. 2021;22. Article No. bbaa086. doi: 10.1093/bib/bbaa086
  14. Smit A., Hubley R., Green P. RepeatMasker. https://www.repeatmasker.org/ (accessed 15.06.2025).
  15. Bao W., Kojima K.K., Kohany O. Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob. DNA. 2015;6. Article No. 11. doi: 10.1186/s13100-015-0041-9
  16. Agarwal P., States D.J. The Repeat Pattern Toolkit (RPT): analyzing the structure and evolution of the C. elegans genome. Proc. Int. Conf. Intell. Syst. Mol. Biol. 1994;2:1–9.
  17. Bao Z., Eddy S.R. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res. 2002;12:1269–1276. doi: 10.1101/gr.88502
  18. Edgar R.C., Myers E.W. PILER: identification and classification of genomic repeats. Bioinformatics. 2005;21(Suppl 1):i152–i158. doi: 10.1093/bioinformatics/bti1003
  19. Kurtz S., Schleiermacher C. REPuter: fast computation of maximal repeats in complete genomes. Bioinformatics. 1999;15:426–427. doi: 10.1093/bioinformatics/15.5.426
  20. Kurtz S., Choudhuri J.V., Ohlebusch E., Schleiermacher C., Stoye J., Giegerich. REPuter: The manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 2001;29:4633–4642. doi: 10.1093/nar/29.22.4633
  21. Delcher A.L., Kasif S., Fleischmann R.D., Peterson J., White O., Salzberg S.L. Alignment of whole genomes. Nucleic Acids Res. 1999;27:2369–2376. doi: 10.1093/nar/27.11.2369
  22. Volfovsky N., Haas B.J., Salzberg S.L. A clustering method for repeat analysis in DNA sequences. Genome Biol. 2001. V.2. Article No. RESEARCH0027. doi: 10.1186/gb-2001-2-8-research0027
  23. Price A.L., Jones N.C., Pevzner P.A. De novo identification of repeat families in large genomes. Bioinformatics. 2005;21(Suppl 1):i351– i358. doi: 10.1093/bioinformatics/bti1018
  24. Achaz G., Boyer F., Rocha E.P., Viari A., Coissac E. Repseek, a tool to retrieve approximate repeats from large DNA sequences. Bioinformatics. 2007;23:19–21. doi: 10.1093/bioinformatics/btl519
  25. Sharma D., Issac B., Raghava G., Ramaswamy R. Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation. Bioinformatics. 2004;20:1405–1412. doi: 10.1093/bioinformatics/bth103
  26. Pevzner P.A., Tang H., Tesler G. De novo repeat classification and fragment assembly. Genome Res. 2004;14:1786–1796. doi: 10.1101/gr.2395204
  27. Lefebvre A., Lecroq T., Dauchel H., Alexandre J. FORRepeats: detects repeats on entire chromosomes and between genomes. Bioinformatics. 2003;19:319–326. doi: 10.1093/bioinformatics/btf843
  28. Figueroa N., Liu X.,Wang J., Karro J. RAIDER: rapid ab initio detection of elementary repeats. In: Advances in Bioinformatics and Computational Biology. BSB 2013. Eds. Setubal J.C., Almeida N.F. Recife, Pernambuco, Brazil: Springer, 2013. P. 170–180. (Lecture Notes in Computer Science, V. 8213). doi: 10.1007/978-3-319-02624-4_16
  29. Schaeffer C.E., Figueroa N.D., Liu X., Karro J.E. phRAIDER: pattern-hunter based rapid ab initio detection of elementary repeats. Bioinformatics. 2016;32:i209–i215. doi: 10.1093/bioinformatics/btw258
  30. Zheng J., Lonardi S. Discovery of repetitive patterns in DNA with accurate boundaries. In: Fifth IEEE Symposium on Bioinformatics and Bioengineering (BIBE’05). Minneapolis, Minnesota, USA: IEEE, 2005. P. 105–112. doi: 10.1109/BIBE.2005.23
  31. Shi J., Liang C. Generic Repeat Finder: a high-sensitivity tool for genome-wide de novo repeat detection. Plant Physiol. 2019;180:1803–1815. doi: 10.1104/pp.19.00386
  32. Healy J., Thomas E.E., Schwartz J.T., Wigler M. Annotating large genomes with exact word matches. Genome Res. 2003;13:2306–2315. doi: 10.1101/gr.1350803
  33. Morgulis A., Gertz E.M., Schäffer A.A., Agarwala R. WindowMasker: window-based masker for sequenced genomes. Bioinformatics. 2006;22:134–141. doi: 10.1093/bioinformatics/bti774
  34. Kurtz S., Narechania A., Stein J.C., Ware D. A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics. 2008;9. Article No. 517. doi: 10.1186/1471-2164-9-517
  35. Girgis H.Z. Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale. BMC Bioinformatics. 2015;16. Article No. 227. doi: 10.1186/s12859-015-0654-5
  36. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27:573–580. doi: 10.1093/nar/27.2.573
  37. Benson G. Sequence Alignment with Tandem Duplication. J. Comput. Biol. 1997;4:351–367. doi: 10.1089/cmb.1997.4.351
  38. Nazipova N., Teplukhina E. Genome-wide technology for revealing fuzzed megasatellites and extended spaced repeats. In: Proceedings of the International Conference “Mathematical Biology and Bioinformatics”. Ed. V.D. Lakhno. Vol. 10. Pushchino: IMPB RAS, 2024. Paper No. e44. doi: 10.17537/icmbb24.56
  39. Li H., Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–1760. doi: 10.1093/bioinformatics/btp324
  40. Burrows M., Wheeler D.J. A Blocksorting Lossless Data Compression Algorithm. Palo Alto, Calif: Digital Equipment Corporation, 1994. (SRC research reports, V. 124).
  41. Gusfield D. Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. Cambridge: Cambridge University Press, 1997. P. 8ff. doi: 10.1017/CBO9780511574931
  42. Aho A., Corasick M. Efficient string matching: an aid to bibliographic search. Communications of the ACM. 1975;18:333–340. doi: 10.1145/360825.360855
  43. Knuth D.E. The Art of Computer Programming. Boston: Addison-Wesley, 1997;1:Fundamental Algorithms.
  44. McCreight E.M. A space-economic suffix tree construction algorithm. Journal of the ACM. 1976;23:262–272. doi: 10.1145/321941.321946
  45. Ukkonen E. On-line construction of suffix-trees. Algorithmica. 1995;14:249–260. doi: 10.1007/BF01206331
  46. Weiner P. Linear pattern matching algorithms. Proceedings of the 14th IEE Annual Symposium on Switching and Automata Theory. 1973:1–11. doi: 10.1109/SWAT.1973.13
  47. Apostolico A. The Myriad Virtues of Subword Trees. In: Combinatorial Algorithms on Words. Eds. Apostolico A., Galil Z. Berlin, Heidelberg: Springer, 1985. P. 85–96. (NATO ASI Series, V. 12). doi: 10.1007/978-3-642-82456-2_6
  48. Manber U., Myers E.W. Suffix Arrays: A New Method for On-Line String Searches. SIAM J. Comput. 1993;22:935–948. doi: 10.1137/0222058
  49. Ferragina P., Manzini G. Opportunistic data structures with applications. In: Proceedings of the 41st Symposium on Foundations of Computer Science (FOCS 2000). Redondo Beach, CA, USA: IEEE, 2000. P. 390–398. doi: 10.1109/SFCS.2000.892127
  50. Marçais G, Kingsford C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics. 2011;27:764–770. doi: 10.1093/bioinformatics/btr011
  51. Li X., Waterman M.S. Estimating the repeat structure and length of DNA sequences using l-tuples. Genome Research. 2003;13:1916–1922. doi: 10.1101/gr.1251803
  52. Jenike K.M., Campos-Domínguez L., Boddé M., Cerca J., Hodson C.N., Schatz M.C., Jaron K.S. K-mer approaches for biodiversity genomics. Genome Res. 2025;35:219–230. doi: 10.1101/gr.279452.124
  53. Roberts M.D., Davis O., Josephs E.B., Williamson R.J. K-mer-based Approaches to Bridging Pangenomics and Population Genetics. Molecular Biology and Evolution. 2025;42. Article No. msaf047. doi: 10.1093/molbev/msaf047
  54. Campagna D., Romualdi C., Vitulo N., Del Favero M., Lexa M., Cannata N., Valle G. RAP: a new computer program for de novo identification of repeated sequences in whole genomes. Bioinformatics. 2004;21:582–588. doi: 10.1093/bioinformatics/bti03
  55. Gu W., Castoe T.A., Hedges D.J., Batzer M.A., Pollock D.D. Identification of repeat structure in large genomes using repeat probability clouds. Anal. Biochem. 2008;380:77–83. doi: 10.1016/j.ab.2008.05.01
  56. Rahman A., Hallgrímsdóttir I., Eisen M., Pachter L. Association mapping from sequencing reads using k-mers. Elife. 2018;7. Article No. e32920. doi: 10.7554/eLife.32920
  57. Ponsero A.J., Miller M., Hurwitz B.L. Comparison of k-mer-based de novo comparative metagenomic tools and approaches. Microbiome Res. Rep. 2023;2. Article No. 27. doi: 10.20517/mrr.2023.26
  58. Wu D.Y., Ugozzoli L., Pal B.K., Qian J., Wallace R.B. The effect of temperature and oligonucleotide primer length on the specificity and efficiency of amplification by the polymerase chain reaction. DNA Cell Biol. 1991;10:233–238. doi 10.1089/dna.1991.10.233. doi: 10.1089/dna.1991.10.233
  59. Becher H., Sampson J., Twyford A.D. Measuring the invisible: the sequences causal of genome size differences in eyebrights (Euphrasia) revealed by k-mers. Front. Plant Sci. 2022;13. Article No. 818410. doi: 10.3389/fpls.2022.818410
  60. Shajii A., Yorukoglu D., William Yu.Y., Berger B. Fast genotyping of known SNPs through approximate k-mer matching. Bioinformatics. 2016;32:i538–i544. doi: 10.1093/bioinformatics/btw460
  61. Bussi Y., Kapon R., Reich Z. Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy. PLoS One. 2021;16. Article No. e0258693. doi: 10.1371/journal.pone.0258693
  62. Chikhi R., Medvedev P. Informed and automated k-mer size selection for genome assembly. Bioinformatics. 2014;30:31–37. doi: 10.1093/bioinformatics/btt310
Table of Contents
Original Article
Nazipova N.N. Application of Suffix Arrays to Detect Repeats in Genomic Sequences. Ìàthematical biology and bioinformatics. 2025;20(2):348-362. doi: 10.17537/2025.20.348
(published in Russian)

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