SavedAdd your journal

Journals / Journal of Engineering Technology and Applied Sciences / 2022 / Cilt: 7 Sayı: 3

A Novel Method for Determining the Non-cds Region By Using Error-Correcting Codes

Elif Segah Oztas(Karamanoğlu Mehmetbey Üniversitesi)0000-0003-0032-3400
Merve Bulut Yılgör(Altınbaş Üniversitesi)0000-0001-6842-1109
Pages
219–230
Publication Date
2022-12-30
🏛️Bibliographic metadata and full text access for this article are provided via DergiPark.
DergiPark Record ↗
✨

AI Summary & Key Takeaways

AI Insight
⚡ TL;DR(Too Long; Didn't Read)

Moreover, optimal results of the algorithm Fi-noncds matched the best sequence length 8 as in [1].

📌 3 Key Takeaways

🎯
Objective & Hypothesis:Our main motivation question is "Is there any relation between the non-coding region and useless error-correcting codes?".
📊
Key Findings & Data:We get the data of the genes from NCBI [21].
💡
Conclusion & Impact:Moreover, optimal results of the algorithm Fi-noncds matched the best sequence length 8 as in [1].
🔬Design:Araştırma Makalesi
📍Scope:Comprehensive Sample
⚙️Variables:Fi-noncds · non-CDS · error-correcting codes

Abstract

Our main motivation question is "Is there any relation between the non-coding region and useless error-correcting codes?". Then we focused CDS and non-CDS areas instead of exon and intron, because CDS involves in process of synthesis a protein and is involved by exons. We get the data of the genes from NCBI [21]. In this study, we introduce the method Fi-noncds that is used for determining the non-CDS region by using error-correcting codes. We obtained that the error-correction codes that can't correct any codes named zero error-correcting code, placed in non-CDS areas, densely. This result shows that non-CDS regions (non-coding areas in DNA) match zero error-correcting codes (useless error-correcting code). Frame lengths 7,8,9 and 10,11,12,13 and 14 were tested by the method. Optimal result for selected genes (TRAV1-1, TRAV1-2, TRAV2, TRAV7, WRKY33, HY5, GR-RBP2) is frame length 8, n=7, k=2, dnaNo=1. Moreover, optimal results of the algorithm Fi-noncds matched the best sequence length 8 as in [1].

🔖

Cite This Article

Oztas, E. S., Yılgör, M. B. (2022). A Novel Method for Determining the Non-cds Region By Using Error-Correcting Codes. Journal of Engineering Technology and Applied Sciences, Cilt: 7 Sayı: 3, 219–230. https://doi.org/10.30931/jetas.1192924

📄 Full Text PDF Viewer

📄

PDF görüntüleyici hazırlanıyor...

References (32)

  1. Lichtenberg, J., Yilmaz, A., Welch, J. D., Kurz, K., Liang, X., Drews, F., Ecker, K., Lee, S. S., Geisler, M., Grotewold, E. and Welch, L. R., "The word landscape of the non-coding segments of the Arabidopsis thaliana genome", Bell Labs Tech. J 10(1).
  2. Forsdyke, D.R., "Are introns in-series error-detecting sequences?", Journal of Theoretical Biology, 93(4) (1981): 861-866.
  3. Forsdyke, D.R., "Conservation of stem-loop potential in introns of snake venom phospholipase A2 genes: An application of FORS-D analysis", 12(6) (1995): 1157 – 1165.
  4. Oztas, E. S., Siap, I., "Lifted polynomials over F-16 and their applications to DNA Codes", Filomat. 27 (2013): 459-466.
  5. Abulraub, T., Ghrayeb A., Nian Zeng, X., "Construction of cyclic codes over GF(4) for DNA computing", J. Franklin Inst. 343(4-5) (2006): 448-457.
  6. Adleman, L. "Molecular computation of solutions to combinatorial problems", Science. 266 (5187) (1994): 1021-1024.
  7. Bayram, A., Oztas, E.S., Siap, I., "Codes over F_4 + v F_4 and some DNA applications", Des. Codes Cryptogr. 80 (2) (2015): 379-393.
  8. Faria, L.C., Rocha, A.S., Kleinschmidt, J.H., Silva--Filho, M. C., Bim, E., Herai, R. H., Yamagishi, M. E., Palazzo, R. Jr., "Is a genome a codeword of an error--correcting code?", PloS one. 7 (5) e36644 (2012).
  9. Grassl, M., Bounds on the minimum distance of linear codes and quantum codes. http://www.codetables.de.
  10. Liebovitch, L.S., Tao, Y., Todorov, A.T., Levine, L., "Is there an error correcting code in the base sequence in DNA?", Biophys J. 71(3) (1996): 1539-1544.
  11. Oztas, E.S., Siap, I., "On a generalization of lifted polynomials over finite fields and their applications to DNA codes" Int. J. Comput. Math. 92 (9) (2015): 1976-1988.
  12. Oztas, E. S., Yildiz, B., Siap, I. "On DNA codes from a family of chain rings", J. Algebra Comb. Discrete Struct. Appl. 4 (1) (2017): 93-102.
  13. Rosen, G. L.: "Examining Coding Structure and Reducdancy in DNA", IEEE Engineering in Medicine and Biology Magazine. 25 (2006): 62-68.
  14. Siap, I., Abulraub, T., Ghrayeb, A., "Cyclic DNA codes over the ring F_2 [u]/(u^2-1) based on the deletion distance" J. Franklin Inst. 346 (8) (2009): 731-740.
  15. Wong, G. K. and Passey, D. A., Huang, Y., Yang, Z. and Yu,J,, "Is "junk" DNA mostly intron DNA?", Genome research, 10 (11) (2000).
  16. NCBI, Database of The Consensus CDS (CCDS) project, https://www.ncbi.nlm.nih.gov/projects/CCDS.
  17. Bulut Yilgor, M. "Cyclic codes over the ring F_2+uF_2+vF_2+v^2 F_2 and their applications to DNA codes", Phd thesis (2020).
  18. Bulut Yılgör, M., Gürsoy, F., Oztas, E.S. et al., "Cyclic codes over F_2+uF_2+vF_2+v^2 F_2 with respect to the homogeneous weight and their applications to DNA codes" AAECC 32 (2021): 621–636.
  19. Brandão, M. M. et al., "Ancient DNA sequence revealed by error-correcting codes" Sci. Rep. 5, 12051; doi: 10.1038/srep12051 (2015).
  20. Vajda, S. and Beglov, D., Wakefield, AE, Egbert, M. and Whitty, A., "Cryptic binding sites on proteins: definition, detection, and druggability", Curr Opin Chem Biol., 44 (2018).
  21. Gene [Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; 2004 – [cited 2022 march 10]. Available from: https://www.ncbi.nlm.nih.gov/gene/.
  22. Forsdyke, D.R., "Are introns in-series error-detecting sequences?", Journal of Theoretical Biology, 93(4) (1981): 861-866.
  23. Forsdyke, D.R., "Conservation of stem-loop potential in introns of snake venom phospholipase A2 genes: An application of FORS-D analysis", 12(6) (1995): 1157 – 1165.
  24. Oztas, E. S., Siap, I., "Lifted polynomials over F-16 and their applications to DNA Codes", Filomat. 27 (2013): 459-466.
  25. Abulraub, T., Ghrayeb A., Nian Zeng, X., "Construction of cyclic codes over GF(4) for DNA computing", J. Franklin Inst. 343(4-5) (2006): 448-457.
  26. Adleman, L. "Molecular computation of solutions to combinatorial problems", Science. 266 (5187) (1994): 1021-1024.
  27. Liebovitch, L.S., Tao, Y., Todorov, A.T., Levine, L., "Is there an error correcting code in the base sequence in DNA?", Biophys J. 71(3) (1996): 1539-1544.
  28. Oztas, E.S., Siap, I., "On a generalization of lifted polynomials over finite fields and their applications to DNA codes" Int. J. Comput. Math. 92 (9) (2015): 1976-1988.
  29. Oztas, E. S., Yildiz, B., Siap, I. "On DNA codes from a family of chain rings", J. Algebra Comb. Discrete Struct. Appl. 4 (1) (2017): 93-102.
  30. Rosen, G. L.: "Examining Coding Structure and Reducdancy in DNA", IEEE Engineering in Medicine and Biology Magazine. 25 (2006): 62-68.
  31. Siap, I., Abulraub, T., Ghrayeb, A., "Cyclic DNA codes over the ring F_2 [u]/(u^2-1) based on the deletion distance" J. Franklin Inst. 346 (8) (2009): 731-740.
  32. Bulut Yılgör, M., Gürsoy, F., Oztas, E.S. et al., "Cyclic codes over F_2+uF_2+vF_2+v^2 F_2 with respect to the homogeneous weight and their applications to DNA codes" AAECC 32 (2021): 621–636.