Russian version English version
Volume 10   Issue 2   Year 2015
Kutyrkin V.A., Chaley M.B.

Structural-Statistical Properties of DNA Coding Regions

Mathematical Biology & Bioinformatics. 2015;10(2):387-397.

doi: 10.17537/2015.10.387.

References

  1. Trifonov E.N., Sussman J.L. The pitch of chromatin DNA is reflected in its nucleotide sequence. Proc. Natl. Acad. Sci. USA. 1980;77:3816-3820. doi: 10.1073/pnas.77.7.3816
  2. Shepherd J.C. Periodic correlations in DNA sequences and evidence suggesting their evolutionary origin in a comma-less genetic code. J. Mol. Evol. 1981;17:94-102. doi: 10.1007/BF01732679
  3. Fickett J.W. Recognition of protein coding regions in DNA sequences. Nucleic Acids Res. 1982;10:5303-5318. doi: 10.1093/nar/10.17.5303
  4. Fickett J.W., Tung C.S. Assessment of protein coding measures. Nucleic Acids Res. 1992;20:6441-5640. doi: 10.1093/nar/20.24.6441
  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;13:63-270. doi: 10.1093/bioinformatics/13.3.263
  6. Grosse I., Herzel H., Buldyrev S.V., Stanley H.E. Species independence of mutual information in coding and noncoding DNA. Phys. Rev. E. 2000;61:5624-5629. doi: 10.1103/PhysRevE.61.5624
  7. Yin C., Yau S.S.T. Prediction of protein coding regions by the 3-base periodicity analysis of a DNA sequence. J. Theor. Biol. 2007;247:687-694. doi: 10.1016/j.jtbi.2007.03.038
  8. Wang L., Stein L.D. Localizing triplet periodicity in DNA and cDNA sequences. BMC Bioinformatics. 2010;11. doi: 10.1186/1471-2105-11-550
  9. Marhon S.A., Kremer S.C. Gene prediction based on DNA spectral analysis: a literature review. J. Comput. Biol. 2011;18:639-676. doi: 10.1089/cmb.2010.0184
  10. Hua W., Wang J., Zhao J. Discrete Ramanujan transform for distinguishing the protein coding regions from other regions. J. Mol. Cell Probes. 2014;28:228-236. doi: 10.1016/j.mcp.2014.04.002
  11. Yin C. Representation of DNA sequences in genetic codon context with applications in exon and intron prediction. J. Bioinform. Comput. Biol. 2015;13(2). doi: 10.1142/S0219720015500043
  12. Chaley M., Kutyrkin V., Tulbasheva G., Teplukhina E., Nazipova N. HeteroGenome: database of genome periodicity. Database. 2014;2014:1-18. doi: 10.1093/database/bau040
  13. Chaley M., 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
  14. Chaley M.B., Kutyrkin V.A. Structure of proteins and latent periodicity in their genes. Moscow Univ. Biol. Sci. Bull. 2010;65(4):133-135. doi: 10.3103/S0096392510040012
  15. Chaley M., Kutyrkin V. Profile-Statistical periodicity of DNA coding regions. DNA Res. 2011;18:353-362. doi: 10.1093/dnares/dsr023
  16. Chaley M.B., Kutyrkin V.A. Recognition of latent periodicity in DNA sequences. Mathematical Biology and Bioinformatics. 2013;8(2):502-512 (in Russ.). doi: 10.17537/2013.8.502
  17. Kutyrkin V.A., Chaley M.B. 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.).
  18. Kutyrkin V.A., Chaley M.B. Spectral-statistical approach to latent profile periodicity recognition in DNA sequences. Mathematical Biology and Bioinformatics. 2014;9(1):33-62. doi: 10.17537/2014.9.33
  19. Kanehisa M., Goto S., Sato Y., Furumichi M., Tanabe M. KEGG for integration and interpretation of large-scale molecular datasets. Nucleic Acids Res. 2012;40(D1):D109-D114. doi: 10.1093/nar/gkr988
Table of Contents Original Article
Math. Biol. Bioinf.
2015;10(2):387-397
doi: 10.17537/2015.10.387
published in Russian

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

 

  Copyright IMPB RAS © 2005-2024