Russian version English version
Volume 8   Issue 2   Year 2013
Chaley M.B., Kutyrkin V.A., Tyulbasheva G.E., Teplukhina E.I., Nazipova N.N.

Investigation of Latent Periodicity Phenomenon in the Genomes of Eukaryotic Organisms

Mathematical Biology & Bioinformatics. 2013;8(2):480-501.

doi: 10.17537/2013.8.480.

References

  1. Richard GF, Kerrest A, Dujon B. Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiol. Mol. Biol. Rev. 2008;72:686-727. doi: 10.1128/MMBR.00011-08
  2. Kelkar YD, Strubczewski N, Hile SE, Chiaromonte F, Eckert KA, Makova KD. What is a microsatellite: a computational and experimental definition based upon repeat mutational behavior at A/T and GT/AC repeats. Genome Biol. Evol. 2010;2:620-635. doi: 10.1093/gbe/evq046
  3. Ellegren H. Microsatellites: simple sequences with complex evolution. Nat. Rev. Genet. 2004;5:435-445. doi: 10.1038/nrg1348
  4. Welch JW, Maloney DH, Fogel S. Unequal crossing-over and gene conversion at the amplified CUP1 locus of yeast. Mol. Gen. Genet. 1990;222:304-310. doi: 10.1007/BF00633833
  5. Tyler-Smith C, Willard H.F. Mammalian chromosome structure. Curr. Opin. Genet. Dev. 1993;3:390-397. doi: 10.1016/0959-437X(93)90110-B
  6. Hewett DR, Handt O, Hobson L, Mangelsdorf M, Eyre HJ, Baker E, Sutherland GR, Schuffenhauer S, Mao JI, Richards RI. FRA10B structure reveals common elements in repeat expansion and chromosomal fragile site genesis. Mol. Cell. 1998;1:773-781. doi: 10.1016/S1097-2765(00)80077-5
  7. Yu S, Mangelsdorf M, Hewett D, Hobson L, Baker E, Eyre HJ, Lapsys N, Le Paslier D, Doggett NA, Sutherland GR, Richards RI. Human chromosomal fragile site FRA16B is an amplified AT-rich minisatellite repeat. Cell. 1997;88:367-374. doi: 10.1016/S0092-8674(00)81875-9
  8. Fu YH, Kuhl DP, Pizzuti A, Pieretti M, Sutcliffe JS, Richards S, Verkerk AJ, Holden JJ, Fenwick RG Jr, Warren ST et al. Variation of the CGG repeat at the fragile X site results in genetic instability: resolution of the Sherman paradox. Cell. 1991;67:1047-1058. doi: 10.1016/0092-8674(91)90283-5
  9. Liquori CL, Ricker K, Moseley ML, Jacobsen JF, Kress W, Naylor SL, Day JW, Ranum LP. Myotonic dystrophy type 2 caused by a CCTG expansion in intron 1 of ZNF9. Science. 2001;293:864-867. doi: 10.1126/science.1062125
  10. Matsuura T, Fang P, Pearson CE, Jayakar P, Ashizawa T, Roa BB, Nelson DL. Interruptions in the expanded ATTCT repeat of spinocerebellar ataxia type 10: repeat purity as a disease modifier? Am. J. Hum. Genet. 2006;78:125-129. doi: 10.1086/498654
  11. Lalioti MD, Scott HS, Buresi C, Rossier C, Bottani A, Morris MA, Malafosse A, Antonarakis SE. Dodecamer repeat expansion in cystatin B gene in progressive myoclonus epilepsy. Nature. 1997;386:847-851. doi: 10.1038/386847a0
  12. Martin P, Makepeace K, Hill SA, Hood DW, Moxon ER. Microsatellite instability regulates transcription factor binding and gene expression. Proc. Natl. Acad. Sci. USA. 2005;102:3800-3804. doi: 10.1073/pnas.0406805102
  13. 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
  14. Reneker J, Shyu CR, Zeng P, Polacco JC, Gassmann W. ACMES: fast multiple-genome searches for short repeat sequences with concurrent cross-species information retrieval. Nucleic Acids Res. 2004;32:W649-W653. doi: 10.1093/nar/gkh455
  15. Roset R, Subirana JA, Messeguer X. MREPATT: detection and analysis of exact consecutive repeats in genomic sequences. Bioinformatics. 2003;19:2475-2476. doi: 10.1093/bioinformatics/btg326
  16. Parisi V, Fonzo VD, Aluffi-Pentini F. STRING: finding tandem repeats in DNA sequences. Bioinformatics. 2003;19:1733-1738. doi: 10.1093/bioinformatics/btg268
  17. Kolpakov R, Kucherov G. Mreps: efficient and flexible detection of tandem repeats in DNA. Nucleic Acids Res. 2003;31:3672-3678. doi: 10.1093/nar/gkg617
  18. Wexler Y, Yakhini Z, Kashi Y, Geiger D. Finding approximate tandem repeats in genomic sequences. J. Comput. Biol. 2005;12:928-942. doi: 10.1089/cmb.2005.12.928
  19. Boeva V, Regnier M, Papatsenko D, Makeev V. Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression. Bioinformatics. 2006;22:676-684. doi: 10.1093/bioinformatics/btk032
  20. Mudunuri SB, Nagarajaram HA. IMEx: imperfect microsatellite extractor. Bioinformatics. 2007;23:1181-1187. doi: 10.1093/bioinformatics/btm097
  21. Pellegrini M, Renda ME, Vecchio A. TRStalker: an efficient heuristic for finding fuzzy tandem repeats. Bioinformatics. 2010;26:i358-i366. doi: 10.1093/bioinformatics/btq209
  22. Sokol D, Benson G, Tojeira J. Tandem repeats over the edit distance. Bioinformatics. 2007;23:e30-e35. doi: 10.1093/bioinformatics/btl309
  23. Sokol D, Atagun F. TRedD – A database for tandem repeats over the edit distance. Database. 2010. Article ID baq003. doi: 10.1093/database/baq003
  24. Gelfand Y, Rodriguez A, Benson G. TRDB – the Tandem Repeats Database. Nucleic Acids Res. 2007;35:80-87. doi: 10.1093/nar/gkl1013
  25. Boby T, Patch A, Aves S. TRbase: a database relating tandem repeats to disease genes for the human genome. Bioinformatics. 2005;21:860-921. doi: 10.1093/bioinformatics/bti059
  26. Chaley MB, Nazipova NN, Kutyrkin VA. Statistical methods for detecting latent periodicity patterns in biological sequences: the case of small-size samples. Pattern Recogn. Image Anal. 2009;19:358-367. doi: 10.1134/S1054661809020217
  27. 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: 10.17537/2007.2.20
  28. Chaley Μ, Kutyrkin V. Model of perfect tandem repeat with random pattern and empirical homogeneity testing poly-criteria for latent periodicity revelation in biological sequences. Math. Biosci. 2008;211:186-204. doi: 10.1016/j.mbs.2007.10.008
  29. Fields S, Johnston M. Cell biology. Whither model organism research? Science. 2005;307:1885-1886. doi: 10.1126/science.1108872
  30. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature. 2001;409:860-921. doi: 10.1038/35057062
Table of Contents Original Article
Math. Biol. Bioinf.
2013;8(2):480-501
doi: 10.17537/2013.8.480
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References Translation into English
Math. Biol. Bioinf.
2018;13(Suppl.):t84-t103
doi: 10.17537/2018.13.t84

Full text (eng., pdf)

 

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