Russian version English version
Volume 8   Issue 2   Year 2013
Chaley M.B., Kutyrkin V.A.

Recognition of Latent Periodicity in DNA Sequences

Mathematical Biology & Bioinformatics. 2013;8(2):502-512.

doi: 10.17537/2013.8.502.

References

  1. Korotkov EV, Korotkova MA, Tulko JS. Latent sequence periodicity of some oncogenes and DNA-binding protein genes. CABIOS. 1997;13:37-44. doi: 10.1093/bioinformatics/13.1.37
  2. Korotkov EV, Korotkova MA, Kudryashov NA. Information decomposition method for analysis of symbolical sequences. Physical Letters A. 2003;312:198-210. doi: 10.1016/S0375-9601(03)00641-8
  3. Shelenkov A, Korotkov A, Korotkov E. MMsat-a database of potential micro-and minisatellites. Gene. 2008;409:53-60. doi: 10.1016/j.gene.2007.11.007
  4. Shelenkov A, Skryabin K, Korotkov E. Search and classification of potential minisatellite sequences from bacterial genomes. DNA Res. 2006;13:89-102. doi: 10.1093/dnares/dsl004
  5. Tiwari S, Ramachandran S, Bhattacharya A, Bhattacharya S, Ramaswamy R. Prediction of probable genes by Fourier analysis of genomic sequences. Comput. Appl. Biosci. 1997;13:263-270. doi: 10.1093/bioinformatics/13.3.263
  6. Issac B, Singh H, Kaur H, Raghava GPS. Locating probable genes using Fourier transform approach. Bioinformatics. 2002;18:196-197. doi: 10.1093/bioinformatics/18.1.196
  7. Sharma D, Issac B, Raghava GPS, Ramaswamy R. Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation. Bioinformatics. 2004;20:1404-1412. doi: 10.1093/bioinformatics/bth103
  8. Lobzin VV, Chechetkin VR. Order and correlations in genomic DNA sequences. The spectral approach. Phys. Usp. 2000;170:57-81 (in Russ.). doi: 10.3367/UFNr.0170.200001c.0057
  9. 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. doi: 10.17537/2007.2.20
  10. 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
  11. 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
  12. Gelfand Y, Rodriguez A, Benson G. TRDB - the Tandem Repeats Database. Nucleic Acids Res. 2007;35:80-87. http://tandem.bu.edu/cgi-bin/trdb/trdb.exe (accessed 31 July 2013). doi: 10.1093/nar/gkl1013
  13. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucl. Acids Res. 1999;27:573-580. doi: 10.1093/nar/27.2.573
  14. Chaley MB, Kutyrkin VA, Tuylbasheva GE, Teplukhina EI, Nazipova NN. Investigation of Latent Periodicity Phenomenon in the Genomes of Eukaryotic Organisms. Mathematical Biology and Bioinformatics. 2013;8(2):480-501. doi: 10.17537/2013.8.480
  15. Cramer H. Mathematical methods of statistics. Stockholm; 1946.
  16. Chaley MB, Kutyrkin VA. Structure of proteins and latent periodicity in their genes. Moscow Univ. Biol. Sci. Bull. 2010;65:133-135. doi: 10.3103/S0096392510040012
  17. Chaley M, Kutyrkin V. Profile-Statistical Periodicity of DNA Coding Regions. DNA Res. 2011;18:353-362. doi: 10.1093/dnares/dsr023
  18. Kutyrkin VA, Chaley MB. Vestnik MGTU im. N.E.Baumana (Herald of the Bauman Moscow State Technical University). 2011;Special Issue 2:200-215 (Natural Sciences Series) (in Russ.).
  19. Kutyrkin VA, Chaley MB. Vestnik MGTU im. N.E.Baumana (Herald of the Bauman Moscow State Technical University). 2012;Special Issue 3:146-157 (Natural Sciences Series) (in Russ.).
  20. FTG: Fast Fourier Transform based GENE Prediction Server. http://www.imtech.res.in/raghava/ftg/ (accessed 31 July 2013).
Table of Contents Original Article
Math. Biol. Bioinf.
2013;8(2):502-512
doi: 10.17537/2013.8.502
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References

 

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