Search and classification of potential minisatellite sequences from bacterial genomes

DNA Research

Volumn 13, Issue 3, 2006, Pages 89-102

  Shelenkov, Andrew ^a   Skryabin, Konstantin ^a   Korotkov, Eugene ^a  

^a INSTITUTE OF BIOENGINEERING   (Russian Federation)

Author keywords

Bacterial genomes; Information decomposition; Minisatellites; Modified profile analysis

Indexed keywords

DINUCLEOTIDE; DNA BASE; DNA MINISATELLITE;

ALGORITHM; ARTICLE; BACTERIAL GENOME; BRADYRHIZOBIUM JAPONICUM; COMPUTER PROGRAM; DATA BASE; DNA SEQUENCE; ESCHERICHIA COLI; FOURIER TRANSFORMATION; HELICOBACTER PYLORI; MONTE CARLO METHOD; NONHUMAN; NUCLEOTIDE SEQUENCE; PERIODICITY; POLYMERASE CHAIN REACTION; PROBABILITY; SEQUENCE HOMOLOGY; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE; VARIABLE NUMBER OF TANDEM REPEAT; XANTHOMONAS CAMPESTRIS;

ANIMALS; DATABASES, FACTUAL; DNA, BACTERIAL; GENOME, BACTERIAL; HUMANS; MATHEMATICS; MINISATELLITE REPEATS; MODELS, GENETIC; SEQUENCE ALIGNMENT;

BACTERIA (MICROORGANISMS);

EID: 33750078973     PISSN: 13402838     EISSN: 13402838     Source Type: Journal    
DOI: 10.1093/dnares/dsl004     Document Type: Article

References (44)

1. Wells, R. 1996, Molecular basis of genetic instability of triplet repeats, J. Biol. Chem., 271, 2875-2878.
2. Weitzmann, M., Woodford, K., and Usdin, K. 1997, DNA secondary structures and the evolution of hypervariable tandem arrays, J. Biol. Chem., 272, 9517-9523.
3. Richards, R., Holman, K., Yu, S., and Sutherland, G. 1993, Fragile X syndrome unstable element, p(CCG)n, and other simple tandem repeat sequences are binding sites for specific nuclear proteins, Hum. Mol. Genet., 2, 1429-1435.
4. Lu, Q., Wallrath, L., Granok, H., and Elgin, S. 1993, (CT)n (GA)n repeats and heat shock elements have distinct roles in chromatin structure and transcriptional activation of the Drosophila hsp26 gene, Mol. Cell. Biol., 13, 2802-2814.
5. Keim, P., Price, L. B., Klevytska, A. M., et al. 2000, Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis, J. Bacteriol., 182, 2928-2936.
6. Frothingham, R. and Meeker-O'Connell, W. A. 1998, Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats, Microbiology, 144, 1189-1196.
7. Supply, P., Mazars, E., Lesjean, S., Vincent, V., Gicquel, B., and Locht, C. 2000, Variable human minisatellite-like regions in the Mycobacterium tuberculosis genome, Mol. Microbiol., 36, 762-771.
8. Le Fleche, P., Hauck, Y., Onteniente, L., et al. 2001, A tandem repeats database for bacterial genomes: application to the genotyping of Yersinia pestis and Bacillus anthracis, BMC Microbiology, 1, 2.
9. Toth, G., Gaspari, Z., and Jurka, J. 2000, Microsatellites in different eukaryotic genomes: survey and analysis, Genome Res., 10, 967-981.
10. Gur-Arie, R., Cohen, C. J., Eitan, Y., Shelef, L., Hallerman, E. M., and and Kashi, Y. 2000, Simple sequence repeats in Escherichia coli: abundance, distribution, composition, and polymorphism, Genome Res., 10, 62-71.
11. Dib, C., Faure, S., Fizames, C., et al. 1996, A comprehensive genetic map of the human genome based on 5,264 microsatellites, Nature, 380, 149-152.
12. van Belkum, A., Scherer, S., van Leeuwen, W., Willemse, D., van Alphen, L., and Verbrugh, H. 1997, Variable number of tandem repeats in clinical strains of Haemophilus influenzae, Infect. Immun., 65, 5017-5027.
13. Adair, D. M., Worsham, P. L., Hill, K. K., et al. 2000, Diversity in a variable-number tandem repeat from Yersinia pestis, J. Clin. Microbiol., 38, 1516-1519.
14. Benson, G. 2001, Tandem cyclic alignment, Proceedings of the 12th annual symposium on combinatorial pattern matching, LNCS, 2089, 118-130.
15. Benson, G. 1999, Tandem repeats finder: a program to analyze DNA sequences, Nucleic Acids Res., 27, 573-580.
16. Kolpakov, R., Bana, G., and Kucherov, G. 2003, mreps: efficient and flexible detection of tandem repeats in DNA, Nucleic Acids Res., 31, 3672-3678.
17. Ruitberg, C. M., Reeder, D. J., and Butler, J. M. 2001, STRBase: a short tandem repeat DNA database for the human identity testing community, Nucleic Acids Res., 29, 320-322.
18. Boby, T., Patch, A.-M., and Aves, S. J. 2005, TRbase: a database relating tandem repeats to disease genes for the human genome, Bioinformatics, 21, 811-816.
19. Korotkov, E. V., Korotkova, M. A., and Kudryashov, N. A. 2003, Information decomposition method to analyze symbolical sequences, Phys. Lett. A, 312, 198-210.
20. Frenkel, F. E., Chaley, M. B., Korotkov, E. V., and Skryabin, K. G. 2004, Evolution of tRNA-like sequences and genome variability, Gene, 335, 57-71.
21. Korotkov, E. V., Korotkova, M. A., and Rudenko, V. M. 2000, MIR: family of repeats common for vertebrate genomes, Mol. Biol. (Mosk), 34, 553-559.
22. Dodin, G., Vandergheynst, P., Levoir, P., Cordier, C., and Marcourt, L. 2000, Fourier and wavelet transform analysis, a tool for visualizing regular patterns in DNA sequences, J. Theor. Biol., 206, 323-326.
23. Korotkova, M. A., Korotkov, E. V., and Rudenko, V. M. 1999, Latent periodicity of protein sequences, J. Mol. Model., 5, 103-115.
24. Korotkov, E. V., Korotkova, M. A., and Tulko, J. S. 1997, Latent sequence periodicity of some oncogenes and DNA-binding protein genes, CABIOS, 13, 37-44.
25. Chaley, M. B., Korotkov, E. V., and Skryabin, K. G. 1999, Method revealing latent periodicity of the nucleotide sequences modified for a case of small samples, DNA Res., 6, 153-163.
26. Kullback, S. 1959, Information Theory and Statistics, John Wiley & Sons, New York.
27. Ward, J. H. 1963, Hierarchical grouping to optimize an objective function, J. Amer. Stat. Assoc., 58, 236-244.
28. Waterman, M. S. 1995, Introduction to Computational Biology. Map, Sequences and Genomes, Chapman & Hall, London.
29. Gribskov, M., McLachlan, A. D., and and Eisenberg, D. 1987, Profile analysis: detection of distantly related proteins, Proc. Natl Acad. Sci. USA, 84, 4355-4358.
30. Sibbald, P. R. and Argos, P. 1990, Weighting aligned protein or nucleic acid sequences to correct for unequal representation, J. Mol. Biol., 216, 813-818.
31. Smith, T. F. and Waterman, M. S. 1981, Identification of common molecular subsequences, J. Mol. Biol., 147, 195-197.
32. Webber, C. and Barton, G. J. 2001, Estimation of P-values for global alignments of protein sequences, Bioinformatics, 17, 1158-1167.
33. Coggins, L. W. and O'Prey, M. 1989, DNA tertiary structures formed in vitro by misaligned hybridization of multiple tandem repeat sequences, Nucleic Acids Res., 17, 7417-7426.
34. Rice, P., Longden, I., and Bleasby, A. 2000, EMBOSS: The European molecular biology open software suite, Trends Genet., 16, 276-277.
35. Kannan, S. K. and Myers, E. W. 1996, An algorithm for locating nonoverlapping regions of maximum alignment score, SIAM J. Comput., 25, 648-662.
36. Benson, G. 1995, A space ef.cient algorithm for finding the best nonoverlapping alignment score, Theor. Comput. Sci., 145, 357-369.
37. Schmidt, J. P. 1998, All highest scoring paths in weighted grid graphs and their application to finding all approximate repeats in strings, SIAM J. Comput., 27, 972-992.
38. Laskin, A. A., Kudryashov, N. A., Skryabin, K. G., and Korotkov, E. V. 2005, Latent periodicity of serine-threonine and tyrosine protein kinases and other protein families, Comput. Biol. Chem., 29, 229-243.
39. Issac, B., Singh, H., Kaur, H., and Raghava, G. P. S. 2002, Locating probable genes using fourier transform approach, Bioinformatics, 18, 196-197.
40. Chechetkin, V. R. and Lobzin, V. V. 1998, Nucleosome units and hidden periodicities in DNA sequences, J. Biomol. Struct. Dyn., 15, 937-947.
41. Jackson, J. H., George, R., and Herring, P. A. 2000, Vectors of Shannon information from Fourier signals characterizing base periodicity in genes and genomes, Biochem. Biophys. Res. Commun., 268, 289-292.
42. Milosavljevic, A. and Jurka, J. 1993, Discovering simple DNA sequences by the algorithmic significance method, CABIOS, 9, 407-411.
43. Landau, G., Schmidt, J., and Sokol, D. 2001, An algorithm for approximate tandem repeats, J. Comp. Biol., 8, 1-18.
44. Subramanian, S., Mishra, R. K., and Singh, L. 2003, Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions, Genome Biol., 4, R13.