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

Öz

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].

Anahtar Kelimeler

• Fi-noncds
• non-CDS
• error-correcting codes
• zero error-correcting codes

Kaynakça

1. [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. [2]Forsdyke, D.R., "Are introns in-series error-detecting sequences?", Journal of Theoretical Biology, 93(4) (1981) : 861-866.
3. [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. [4]Oztas, E. S., Siap, I., "Lifted polynomials over F-16 and their applications to DNA Codes", Filomat. 27 (2013) : 459-466.
5. [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. [6]Adleman, L. "Molecular computation of solutions to combinatorial problems", Science. 266 (5187) (1994) : 1021-1024.
7. [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. [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. [9]Grassl, M., Bounds on the minimum distance of linear codes and quantum codes. http://www.codetables.de.
10. [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. [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. [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. [13]Rosen, G. L.: "Examining Coding Structure and Reducdancy in DNA", IEEE Engineering in Medicine and Biology Magazine. 25 (2006) : 62-68.
14. [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. [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. [16]NCBI, Database of The Consensus CDS (CCDS) project, https://www.ncbi.nlm.nih.gov/projects/CCDS.
17. [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. [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. [19]Brandão, M. M. et al., "Ancient DNA sequence revealed by error-correcting codes" Sci. Rep. 5, 12051; doi: 10.1038/srep12051 (2015).
20. [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. [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/.