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Volume 5   Issue 1   Year 2010
Tetuev R.K., Nazipova N.N., Pankratov A.N., Dedus F.F.

Search for Megasatellite Tandem Repeats in Eukaryotic Genomes by Estimation of GC-content Curve Oscillations

Mathematical Biology & Bioinformatics. 2010;5(1):30-42.

doi: 10.17537/2010.5.30.


  1. Kramer PR, Pearson CE. Stability of triplet repeats of myotonic dystrophy and fragile X loci in human mutator mismatch repair cell lines. Hum. Genet. 1996;98:151-157.
  2. Mitas M. Trinucleotide repeats associated with human disease. Nucleic Acids Res. 1997;25:2245-2253. doi: 10.1093/nar/25.12.2245
  3. Ranum PWL, Day WJ. Dominantly inherited, non-coding microsatellite expansion disorders. Curr. Opin. Genet. Dev. 2002;12:266-271.
  4. Richards RI, Holman K, Yu S, Sutherland GR. Fragile X syndrome unstable element, P(CCG)N, and other simple tandem repeat sequences are binding-sites for specific nuclear proteins. Hum. Mol. Genet. 1993;2:1429-1435.
  5. Sutherland GR, Richards IR. Simple tandem DNA repeats and human genetic disease. Proc. Natl. Acad. Sci. USA. 1995;92:3636-3641.
  6. Hamada H, Seidman M, Howard B, Gorman C. Enhanced gene-expression by the poly(DT-DG) poly (DC-DA) sequence. Mol. Cell. Biol. 1984;4:2622-2630.
  7. Guerini FR, Ferrante P, Losciale L, Caputo D, Lombardi ML, Pirozzi G, Luongo V, Sudomoina MA, Andreewski TV, Alekseenkov AD, Boiko AN, Gusev EI, Favorova OO. Myelin basis protein gene is associated with ms in DR4- and DR5-positive Italians and Russians. Neurology. 2003;61:520-526. doi: 10.1212/01.WNL.0000079372.54703.A8
  8. Licastro F, Grimaldi LM, Bonafè M, Martina C, Olivieri F, Cavallone L, Giovanietti S, Masliah E, Franceschi C. Interleukin-6 gene alleles affect the risk of Alzheimer’s disease and levels of the cytokine in blood and brain. Neurobiol. Aging. 2003;24:921-926.
  9. Brzustowicz LM, Hodgkinson KA, Chow EW, Honer WG, Bassett AS. Location of a major susceptibility locus for familial schizophrenia on chromosome 1q21–q22. Science. 2000;288:678-682. doi: 10.1126/science.288.5466.678
  10. Sidransky D. Nucleic acid-based methods for the detection of cancer. Science. 1997;278:1054-1058. doi: 10.1126/science.278.5340.1054
  11. Butler J. Forensic DNA Typing: Biology and Technology Behind STR Markers. London: Academic Press; 2003.
  12. Lewin B. Genes. John Wiley and Sons, Inc; 1983.
  13. Kim J, Gordon L, Dehal P, Badri H, Christensen M, Groza M, Ha C, Hammond S, Vargas M, Wehri E, Wagner M, Olsen A, Stubbs L. Homology-driven assembly of sequence-ready mouse BAC contig map spanning regions related to the 46-Mb gene rich euchromatic segments of human chromosome 19. Genomics. 2001;74:129-141. doi: 10.1006/geno.2001.6521
  14. Bailey JA, Yavor AM, Massa HF, Trasl BJ, Eichler EE. Segmental Duplications: Organization and Impact within the Current Human Genome Project Assembly. Genome Res. 2001;11:1005-1017. doi: 10.1101/gr.GR-1871R
  15. Eichler EE. Masquerading repeats: Paralogous pitfalls of the Human Genome. Genome Res. 1998;8:758-762.
  16. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA et al. The sequence of the human genome. Science. 2001;291(5507):1304-1351. doi: 10.1126/science.1058040
  17. Benson G. Tandem repeat finder: a program to analyse DNA sequences. Nucleic Acids Res. 1999;27:573-580. doi: 10.1093/nar/27.2.573
  18. Smit AFA, Hubley R, Green P. RepeatMasker. (accessed 20 April 2010).
  19. UCSC Genome Bioinformatics Site. (accessed 20 April 2010).
  20. Chaley MB, Nazipova NN, Kutyrkin VA. Joint Use of Different Homogeneity Testing Criteria for Latent Periodicity Revelation in Biological Sequences. Mathematical Biology and Bioinformatics. 2007;2(1):20-35 (in Russ.). doi: 10.1134/S1054661809020217
  21. Pankratov AN, Gorchakov MA, Dedus FF, Dolotova NS, Kulikova LI, Makhortykh SA, Nazipova NN, Novikova DA, Olshevets MM, Pyatkov MI, Rudnev VR, Tetuev RK, Filippov VV. Spectral Analysis for Identification and Visualization of Repeats in Genetic Sequences. Pattern Recognition and Image Analysis. 2009;19(4):687-692. doi: 10.1134/S105466180904018X
  22. Kolmogorov AN, Fomin SV. Elements of the Theory of Functions and Functional Analysis. Courier Dover Publications; 1999. 288 p.
  23. Dedus FF, Makhortykh SA, Ustinin MN, Dedus AF. Obobshchennyi spektral'no-analiticheskii metod obrabotki informatsionnykh massivov (The generalized spectral-analytical method of processing data arrays). Moscow; 1999. 356 p. (in Russ.).
  24. Boltnev AA, Kalitkin NN, Kacher OA. The Gibbs Effect in Difference Schemes. Doklady Mathematics. 2006;74(3):921-925. doi: 10.1134/S1064562406060342
  25. Dedus FF, Kulikova LI, Makhortykh SA, Nazipova NN, Pankratov AN, Tetuev RK. Analytical recognition methods for repeated structures in genomes. Doklady Mathematics. 2006;74(3):926-929. doi: 10.1134/S1064562406060354
  26. Dedus FF, Kulikova LI, Pankratov AN, Tetouev RL. Classical Orthogonal Bases in Problems of Analytical Description of Information Signals and Their Processing. Moscow: Faculty of Computational Mathematics and Cybernetics of Moscow State University; 2004 (in Russ.).
  27. Tetuev RL, Dedus FF. Klassicheskie ortogonal'nye polinomy. Primenenie v zadachakh obrabotki dannykh (Classical Orthogonal Polynomials. Application for Solving Problems of Data Processing). Pushchino; 2007 (in Russ.).
  28. Novikova DA, Povolotskii AV. In: Sbornik statei molodykh uchenykh fakul'teta VMiK MGU (Articles of Young Scientists of the Faculty of Computational Mathematics and Cybernetics of the Moscow State University). 2007(4):1-8 (in Russ.).
  29. Press WH, Flannery BP, Teukolsky SA, Vetterling WT. Numerical Recipes in C: The Art of Scientific Computing. Second Edition. Cambridge University Press; 1997. P. 195-196.
  30. She X, Cheng Ze, Zőllner S, Church DM, Eichler EE. Mouse Segmental Duplication and Copy-Number Variation. Nat. Genet. 2008;40:909-914.
  31. Gelfand Ye, Rodriguez A, Benson G. TRDB–The Tandem Repeats Database. Nucleic Acids Res. 2007;35:D80–D87. doi: 10.1093/nar/gkl1013
  32. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogentic and Genome Research. 2005;110:462-467. doi: 10.1159/000084979
  33. Kohany O, Gentles AJ, Hankus L, Jurka J. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics. 2006;7:474. doi: 10.1186/1471-2105-7-474
  34. Tetuev RK, Dedus FF, Nazipova NN, Makhortykh SA, Kulikova LI, Pankratov AN, Ol'shevets MM. Spektral'nyi analiz dannykh, poisk netochnykh periodov v signalakh SpectralRevisor (SpectralRevisor: Spectral Data Analysis and Search for Imperfect Periods in Signals): ROSPATENT evidence Ή2007611639 of official registration of computer programs. 2007 (in Russ.).
Table of Contents Original Article
Math. Biol. Bioinf.
doi: 10.17537/2010.5.30
published in Russian

Abstract (rus.)
Abstract (eng.)
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