May  2017, 11(2): 307-312. doi: 10.3934/amc.2017023

Reversible DNA codes over $F_{16}+uF_{16}+vF_{16}+uvF_{16}$

1. 

Department of Mathematics, Yildiz Technical University, Istanbul, Turkey

2. 

Department of Mathematics, Karamanoglu Mehmetbey University, Karaman, Turkey

3. 

JACODESMATH Institute, Istanbul, Turkey

Received  February 2016 Revised  March 2016 Published  May 2017

In this paper we study the structure of specific linear codes called DNA codes. The first attempts on studying such codes have been proposed over four element rings which are naturally matched with DNA four letters. Later, double (pair) DNA strings or more general $k$-DNA strings called $k$-mers have been matched with some special rings and codes over such rings with specific properties are studied. However, these matchings in general are not straightforward and because of the fact that the reverse of the codewords ($k$-mers) need to exist in the code, the matching problem is difficult and it is referred to as the reversibility problem. Here, $8$-mers (DNA 8-bases) are matched with the ring elements of $R_{16}=F_{16}+uF_{16}+vF_{16}+uvF_{16}.$ Furthermore, cyclic codes over the ring $R_{16}$ where the multiplication is taken to be noncommutative with respect to an automorphism $\theta$ are studied. The preference on the skewness is shown to be very useful and practical especially since this serves as a direct solution to the reversibility problem compared to the commutative approaches.

Citation: Fatmanur Gursoy, Elif Segah Oztas, Irfan Siap. Reversible DNA codes over $F_{16}+uF_{16}+vF_{16}+uvF_{16}$. Advances in Mathematics of Communications, 2017, 11 (2) : 307-312. doi: 10.3934/amc.2017023
References:
[1]

T. AbulraubA. Ghrayeb and X. N. Zeng, Construction of cyclic codes over $GF(4)$ for DNA computing, J. Franklin Inst., 343 (2006), 448-457.  doi: 10.1016/j.jfranklin.2006.02.009.  Google Scholar

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[3]

A. BayramE. S. Oztas and I. Siap, Codes over $F_4 + v F_4$ and some DNA applications, Des.Codes Crypt., 80 (2016), 379-393.  doi: 10.1007/s10623-015-0100-8.  Google Scholar

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F. Gursoy, E. S. Oztas and I. Siap, Reversible DNA codes using skew polynomial rings Appl. Algebra Engrg. Comm. Comput. to appear. Google Scholar

[7]

F. GursoyI. Siap and B. Yildiz, Construction of skew cyclic codes over $F_q + vF_q$, Adv. Math. Commun., 44 (2014), 313-322.  doi: 10.3934/amc.2014.8.313.  Google Scholar

[8]

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[9]

S. JitmanS. Ling and P. Udomkavanich, Skew constacyclic codes over finite chain rings, Adv. Math. Commun., 6 (2012), 29-63.  doi: 10.3934/amc.2012.6.39.  Google Scholar

[10]

J. Lichtenberg, A. Yilmaz, J. Welch, K. Kurz, X. Liang, F. Drews, K. Ecker, S. Lee, M. Geisler, E. Grotewold and L. Welch, The word landscape of the non-coding segments of the Arabidopsis thaliana genome BMC Genomics 10 (2009), 463. Google Scholar

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I. SiapT. AbualrubN. Aydin and P. Seneviratne, Skew cyclic codes of arbitrary length, Int. J. Inf. Coding Theory, 2 (2011), 10-20.  doi: 10.1504/IJICOT.2011.044674.  Google Scholar

[12]

I. SiapT. Abulraub and A. Ghrayeb, Cyclic DNA codes over the ring $F_2[u]/(u^2-1)$ based on the deletion distance, J. Franklin Inst., 346 (2009), 731-740.  doi: 10.1016/j.jfranklin.2009.07.002.  Google Scholar

[13]

E. S. Oztas and I. Siap, Lifted polynomials over $F_{16}$ and their applications to DNA Codes, Filomat, 27 (2013), 459-466.  doi: 10.2298/FIL1303459O.  Google Scholar

[14]

T. YaoM. Shi and P. Solé, Skew cyclic codes over $F_q + uF_q + vF_q + uvF_q$, J. Algebra Comb. Discrete Appl., 2 (2015), 163-168.  doi: 10.13069/jacodesmath.90080.  Google Scholar

[15]

B. Yildiz and I. Siap, Cyclic codes over $F_2[u]/(u^4-1)$ and applications to DNA codes, Comput. Math. Appl., 63 (2012), 1169-1176.  doi: 10.1016/j.camwa.2011.12.029.  Google Scholar

show all references

References:
[1]

T. AbulraubA. Ghrayeb and X. N. Zeng, Construction of cyclic codes over $GF(4)$ for DNA computing, J. Franklin Inst., 343 (2006), 448-457.  doi: 10.1016/j.jfranklin.2006.02.009.  Google Scholar

[2]

L. Adleman, Molecular computation of solutions to combinatorial problems, Science New Ser., 266 (1994), 1021-1024.   Google Scholar

[3]

A. BayramE. S. Oztas and I. Siap, Codes over $F_4 + v F_4$ and some DNA applications, Des.Codes Crypt., 80 (2016), 379-393.  doi: 10.1007/s10623-015-0100-8.  Google Scholar

[4]

D. BoucherW. Geiselmann and F. Ulmer, Skew cyclic codes, Appl. Algebra Eng. Comm., 18 (2007), 379-389.  doi: 10.1007/s00200-007-0043-z.  Google Scholar

[5]

D. BoucherP. Solé and F. Ulmer, Skew constacyclic codes over Galois rings, Adv. Math. Commun., 2 (2008), 273-292.  doi: 10.3934/amc.2008.2.273.  Google Scholar

[6]

F. Gursoy, E. S. Oztas and I. Siap, Reversible DNA codes using skew polynomial rings Appl. Algebra Engrg. Comm. Comput. to appear. Google Scholar

[7]

F. GursoyI. Siap and B. Yildiz, Construction of skew cyclic codes over $F_q + vF_q$, Adv. Math. Commun., 44 (2014), 313-322.  doi: 10.3934/amc.2014.8.313.  Google Scholar

[8]

N. Jacobson, Finite-Dimensional Division Algebras over Fields Springer, Berlin, 1996. doi: 10.1007/978-3-642-02429-0.  Google Scholar

[9]

S. JitmanS. Ling and P. Udomkavanich, Skew constacyclic codes over finite chain rings, Adv. Math. Commun., 6 (2012), 29-63.  doi: 10.3934/amc.2012.6.39.  Google Scholar

[10]

J. Lichtenberg, A. Yilmaz, J. Welch, K. Kurz, X. Liang, F. Drews, K. Ecker, S. Lee, M. Geisler, E. Grotewold and L. Welch, The word landscape of the non-coding segments of the Arabidopsis thaliana genome BMC Genomics 10 (2009), 463. Google Scholar

[11]

I. SiapT. AbualrubN. Aydin and P. Seneviratne, Skew cyclic codes of arbitrary length, Int. J. Inf. Coding Theory, 2 (2011), 10-20.  doi: 10.1504/IJICOT.2011.044674.  Google Scholar

[12]

I. SiapT. Abulraub and A. Ghrayeb, Cyclic DNA codes over the ring $F_2[u]/(u^2-1)$ based on the deletion distance, J. Franklin Inst., 346 (2009), 731-740.  doi: 10.1016/j.jfranklin.2009.07.002.  Google Scholar

[13]

E. S. Oztas and I. Siap, Lifted polynomials over $F_{16}$ and their applications to DNA Codes, Filomat, 27 (2013), 459-466.  doi: 10.2298/FIL1303459O.  Google Scholar

[14]

T. YaoM. Shi and P. Solé, Skew cyclic codes over $F_q + uF_q + vF_q + uvF_q$, J. Algebra Comb. Discrete Appl., 2 (2015), 163-168.  doi: 10.13069/jacodesmath.90080.  Google Scholar

[15]

B. Yildiz and I. Siap, Cyclic codes over $F_2[u]/(u^4-1)$ and applications to DNA codes, Comput. Math. Appl., 63 (2012), 1169-1176.  doi: 10.1016/j.camwa.2011.12.029.  Google Scholar

Table 1.  The $\tau$ mapping between DNA pairs and $F_{16}$ [13]}
$F_{16}$(multiplicative) $F_{16}$(additive) Double DNA pair
0 0 AA
$\alpha^0$ 1 TT
$\alpha^1$ $\alpha$ AT
$\alpha^2$ $\alpha^2$ GC
$\alpha^3$ $\alpha^3$ AG
$\alpha^4$ $1+\alpha$ TA
$\alpha^5$ $ \alpha+\alpha^2$ CC
$\alpha^6$ $\alpha^2 +\alpha^3$ AC
$\alpha^7$ $1+\alpha +\alpha^3$ GT
$\alpha^8$ $1 +\alpha^2$ CG
$\alpha^9$ $\alpha +\alpha^3$ CA
$\alpha^{10}$ $1+\alpha +\alpha^2$ GG
$\alpha^{11}$ $\alpha +\alpha^2+\alpha^3$ CT
$\alpha^{12}$ $1+\alpha +\alpha^2+\alpha^3$ GA
$\alpha^{13}$ $1 +\alpha^2+\alpha^3$ TG
$\alpha^{14}$ $1+\alpha^3$ TC
$F_{16}$(multiplicative) $F_{16}$(additive) Double DNA pair
0 0 AA
$\alpha^0$ 1 TT
$\alpha^1$ $\alpha$ AT
$\alpha^2$ $\alpha^2$ GC
$\alpha^3$ $\alpha^3$ AG
$\alpha^4$ $1+\alpha$ TA
$\alpha^5$ $ \alpha+\alpha^2$ CC
$\alpha^6$ $\alpha^2 +\alpha^3$ AC
$\alpha^7$ $1+\alpha +\alpha^3$ GT
$\alpha^8$ $1 +\alpha^2$ CG
$\alpha^9$ $\alpha +\alpha^3$ CA
$\alpha^{10}$ $1+\alpha +\alpha^2$ GG
$\alpha^{11}$ $\alpha +\alpha^2+\alpha^3$ CT
$\alpha^{12}$ $1+\alpha +\alpha^2+\alpha^3$ GA
$\alpha^{13}$ $1 +\alpha^2+\alpha^3$ TG
$\alpha^{14}$ $1+\alpha^3$ TC
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