Abstract
The main motivation of this work is to study and obtain some reversible and DNA codes of length n with better parameters. Here, we first investigate the structure of cyclic and skew cyclic codes over the chain ring . We show an association between the codons and the elements of using a Gray map. Under this Gray map, we study reversible and DNA codes of length n. Finally, several new DNA codes are obtained that have improved parameters than previously known codes. We also determine the Hamming and the Edit distances of these codes.
1. Introduction
DNA is a nucleic acid used for carrying genetic information in living organisms. It is a double-strand molecule formed from two possible nitrogenous bases—Purines (Adenine and Guanine) and Pyrimidines (Cytosine—and Thymine) and two chemically polar ends, namely, and . The Watson–Crick complementary (WCC) relation, which is characterized as , and vice versa, is used to bind the bases of DNA. In 1994, Adleman [1] discussed the Hamiltonian path problem using DNA molecules. This (NP-complete) problem is solved by encoding a small graph in DNA molecules where all the operations were carried out using standard protocols such as the WCC relation. Due to massive parallelism, DNA computing emerged as a powerful tool among researchers to solve computationally difficult problems. Further, the experiments are performed on synthesized DNA and RNA molecules to control their combinatorial constraints such as constant -content and Hamming distance.
Linear codes over finite fields have been explored for almost three decades, but this research area experienced an astonishing rate after the remarkable work of Hammons et al. [2] when they established a relation between linear codes over with other non-linear binary codes. Afterward, many authors [3,4,5,6] considered alphabets endowed with a ring structure and found many good linear codes over finite fields via specific Gray maps. Within the class of linear codes, cyclic codes are the pivotal and the most studied codes due to their theoretical richness and practical implementation. Recently, many authors [7,8,9,10,11,12,13] constructed DNA codes using cyclic codes over rings. For instance, Bayram et al. [7] and Yildiz and Siap [13] explored DNA codes over the rings , and , respectively. In 2019, Mostafanasab and Darani [12] discussed the structure of cyclic DNA codes over the chain ring . Liu et al. [14] worked on cyclic DNA codes of an odd length over . On the other hand, Boucher et al. [15] introduced skew cyclic codes and discovered many new linear codes. Further, in [16,17], more properties of these codes over chain rings have been established. Recently, Gursoy et al. [18] studied reversible DNA codes by using skew cyclic codes. Later on, Cengellenmis et al. [19] studied DNA codes from skew cyclic codes over the rings . Motivated by the above works, we consider cyclic as well as skew cyclic codes over the finite chain ring to construct DNA codes of arbitrary lengths. Hamming and edit distances are also calculated for the obtained codes. Interestingly, we obtain several new codes with better parameters than known codes [14].
The article is structured as follows: The Gray map, together with the correspondence of the codons and the other basic results of cyclic codes, are in Section 2. Reversible cyclic codes over the ring are covered in Section 3, whereas the reversible skew cyclic codes are studied in Section 4. Some results related to the complement and reverse complement of obtained codes are presented in Section 5. Based on our established results from the previous Sections and magma computer algebra system [20], we provide a few examples of DNA codes of arbitrary lengths in Section 6. In the end, we conclude our work in Section 7.
2. Preliminaries
Let where be a finite field. Then is a finite chain ring with characteristic 2 and every element r of can be represented as where for and . It is easy to show that is a principal ideal ring with unique maximal ideal and is isomorphic to . Recall that the ring has 48 invertible elements of the form , where is invertible in .
A linear code of length n and alphabets from is a submodule of an -module . The elements of are called the codewords. The Hamming weight of an element is defined as = and Hamming distance between any two elements and in is defined as Additionally, the lowest value in the set is considered as the the Hamming distance of the code .
Now, we describe a Gray map as:
where for . It is easy to see that the function is a distance-preserving map and is extendable to component-wise. In Table 1, we establish the connection between the ring elements and the codons by using the Gray map (1).
Table 1.
Codons correspondence with the elements of .
Definition 1.
For a given polynomial , the reciprocal polynomial is denoted by and defined as . A polynomial is said to be self-reciprocal if and only if for some non-zero element b in .
Now, we present some useful lemmas that appeared in [8,14].
Lemma 1.
Let and be polynomials over of degrees r and s, respectively, with . Then:
- 1.
- 2.
- .
Lemma 2.
Let , , and be polynomials over of degrees r, s, and t, respectively, where . Then:
- 1.
- 2.
- .
Using the Watson–Crick complementary relation, we define the reverse (R) and the reverse complement (RC) of a DNA codeword by and , respectively. For example, given , we obtain and .
We have the following observations based on the Gray map provided in Equation (1).
Lemma 3.
- 1.
- For any , we havewhere
- 2.
- where .
3. Reversible Cyclic Codes over
In the present section, we investigate the structure of cyclic codes and prove reversible conditions on these codes. The cyclic codes of odd lengths are provided in [14] and a detailed discussion on cyclic codes of arbitrary length with alphabets from is explored in [6]. Now, in the subsequent theorems, we describe the structure of the cyclic code. We omit the proof due to its similarity to the proof provided in [6].
Theorem 1.
Let be a cyclic code of length n over . Then the code is provided by:
where over , , , and over . Moreover, , , and .
Corollary 1.
If the length of a cyclic code is odd and , then .
A similar result is also possible when n is not odd. In this case, we assume that and consequently obtain the following result.
Corollary 2.
If a cyclic code is of even length n and , then .
When , then and as a subset of . Since the other containment is true by the definition of , we, therefore, obtain the following corollary.
Corollary 3.
For a cyclic code , if , then .
Definition 2.
Given a code over , we define by . Particularly, since , .
In the next result, we determine the Hamming distance of the code by using the above definition in terms of the Hamming distance of .
Theorem 2.
Let be a code provided by . Then Hamming distance of and are equal, i.e.,
Proof.
It can be obtained from [4]. □
Remark 1.
For the sake of brevity, we use b for polynomial whenever belongs to the field .
Lemma 4.
Let of degrees respectively. Then .
Theorem 3.
Let be a cyclic code of even length over with monic polynomials , and of degrees and t, respectively. Then the code is reversible if and only if:
- (1)
- is a self-reciprocal polynomial;
- (2)
- and , where and .
Proof.
Let be a reversible cyclic code. Then
Comparing right side of the two equations, we obtain , and . Now, using , we obtain in and this implies that the polynomial is self-reciprocal. Therefore, where is a non-zero element in . Now comparing the degrees of both sides, we obtain a constant polynomial , say, . We have . Again, comparing the degrees of both sides, we obtain in , say . Thus, and where and .
Conversely, assume (1) and (2) hold. Then
Thus, the code is reversible. □
Theorem 4.
Let be a cyclic code of even length n over with polynomials , , and of degrees , and t, respectively, and . Furthermore, assume that . Then the code is reversible if and only if:
- (1)
- and are self-reversible;
- (2)
- , and where and .
Proof.
Let be a reversible code. Then
Furthermore,
Comparing both equations, we obtain , say , this implies that is self-reciprocal. Therefore, and ; this implies that divides .
Again, and hence implies that is self-reversible.
Conversely, suppose conditions (1) and (2) hold. Then
Therefore, is reversible. □
The following theorem states the reversible condition of odd length codes or a code satisfying Corollary 2.
Theorem 5.
Let be a cyclic code over with . Then code is reversible if and only if polynomials , and are self-reversible.
Proof.
Let be a reversible code. Then for some polynomials in , we have
Comparing both sides, we obtain , say , since , then is self-reciprocal. Similarly, and are self-reciprocal polynomials.
Conversely, let the polynomials , , and be self-reciprocal. Then, elements of are provided by the polynomial therefore by Lemma 4, we have
Thus, is reversible. □
Now, in the following result, we determine the rank of a code . The proof is followed by similar arguments as in Theorem 3 of [6].
Theorem 6.
Let be a cyclic code of length n over such that
where , and are polynomials in and and . Then is a free module and . Moreover, the basis of is provided by the set S, where
4. Reversible Skew Cyclic Codes over
In this part, we focus on the structure of skew cyclic codes over and establish a necessary and sufficient condition for these codes to be reversible. We first define the skew polynomial ring over and provide some definitions that will be used in this section.
Let be defined by . Now, consider a map defined by:
where . Since is an extension of , is an automorphism of . Let us consider the set:
Define the addition on as the usual addition of polynomials and multiplication under the rule . Then, it is easy to show that forms a ring under the above binary operations, known as a skew polynomial ring. Here, unless is identity automorphism.
Definition 3.
Let be a skew cyclic shift operator defined by:
, a linear code of length n over is said to be skew cyclic code if for any codeword , their skew cyclic shift belongs to , that is, .
Definition 4.
For skew polynomials, , the polynomial is said to be rightly divided by if and only if there exists a skew polynomial such that and we denote it by .
Using similar arguments as in the commutative case, we provide the structure of the skew cyclic codes over for automorphism .
Theorem 7.
Let be a skew cyclic code in . Then, with in , and right divides , and .
Proof.
Consider the ring and . For a skew cyclic code over , define a map by . Then, is a ring homomorphism that can be extended to a homomorphism defined by
Then .
In order to determine the generators of cyclic code in , we need to know the image of which is a skew cyclic code in .
Let D be a cyclic code in . Now, define a map by . Then is a ring homomorphism. We extend to a ring homomorphism defined by
Then,
Since the set image() is also an ideal and hence a skew cyclic code generated by , where right divides . Therefore, where and .
Similarly, the set image() is an ideal over . Therefore, skew cyclic code over is provided by with and , □
Definition 5.
Let be a polynomial in . Then, is said to be a palindromic polynomial if and θ-palindromic if where .
Note that if the length of the code is odd, then the skew cyclic codes and cyclic codes are equivalent (Theorem 8 in [17]). Now, we provide two lemmas to check the reversibility of the even length skew cyclic codes over the field .
Lemma 5.
Let be a skew cyclic code of even length generated by a monic polynomial of even degree, where in . Then, the code is reversible if and only if skew polynomial is θ-palindromic.
Proof.
Let be a skew cyclic code of even length generated by the -palindromic polynomial of even degree m over the ring . Then, the elements of the generated code are provided by . From the repetitive use of Lemma 3, for , we obtain:
where and . Since belongs to the code , is a reversible code.
Conversely, let be a reversible code generated by . Then, because is odd:
Since is a skew cyclic and reversible code,
Further, we obtain , which contradicts the fact that is a minimal degree polynomial in implies . Comparing coefficients, we obtain:
for . Thus, and the polynomial is -palindromic. □
Lemma 6.
Let be a skew cyclic code of even length generated by a monic polynomial of odd degree, where in . Then, the code is reversible if and only if the skew polynomial is palindromic.
Proof.
Let be a skew cyclic code of even length generated by a palindromic polynomial of odd degree m over the ring . Then, elements of the generated code are provided by . From the repetitive use of Lemma 3 and using the property of the palindromic polynomial, for , we obtain:
where and . Since the reverse of belongs to , the code is reversible.
Conversely, let be a reversible code generated by . Since is even:
Furthermore, the code is a skew cyclic as well as reversible code; therefore, and:
This implies that , which contradicts the fact that is a minimal degree polynomial in . Hence, . By comparing the coefficients, we obtain
for . Thus, the given polynomial is palindromic. □
Now, in the next theorem, we provide necessary and sufficient conditions for a skew cyclic code to be reversible in terms of palindromic and -palindromic polynomials. These conditions depend on the degree of generator polynomials of .
Theorem 8.
Let be a skew cyclic code of even length, where right divides in and is even (odd), for . Then, the code is reversible if and only if skew polynomials are θ-palindromic (palindromic) for .
5. DNA Codes over
In this section, we discuss the complementary condition of the codes obtained from previous sections to obtain DNA codes. For a DNA code, the reversible and complement conditions are essential [21].
Definition 6.
Let be a code of length n over . If for all , then or equivalently is called a DNA code.
In the following lemma, we provide some relations on ring elements and their complement using the Gray map provided in Equation (1).
Lemma 7.
For the given cyclic code in Section 3, the following conditions hold:
- (1)
- For any
- (2)
- For any .
Proof.
This lemma can easily be proved by observing Table 1. □
Remark 2.
We identify by the polynomial
Theorem 9.
Given a polynomial in . We have .
Proof.
Let be a reversible-complement code. Then, by definition, is reversible and implies that . That is, is reversible and .
Conversely, let be a polynomial in . Then:
Thus, cyclic code is a reversible-complement code. □
Corollary 4.
Let be a cyclic code of even length over . Then, is a DNA code if and only if is reversible and is in .
Proof.
It is obvious from above theorem. □
6. Computational Results
Now, we provide some examples of DNA codes satisfying the above-mentioned constraints. We consider DNA code of any length (even or odd). All the computational works are performed by using Magma software [20].
Example 1.
In , we have:
Let be a cyclic code of length over provided by:
Then, using Theorem 2, we obtain . Furthermore, does not divide and polynomial is self reciprocal. Thus, we obtain a DNA code of parameters .
In the next example, we provide some DNA codes of arbitrary lengths that are generated from cyclic codes over .
Example 2.
Suppose is a cyclic code of the form where . If , then we list several DNA codes in Table 2 that are obtained from cyclic code . Since , , and are equal, therefore, in Table 2, we mention only . For brevity, polynomial is represented as .
Table 2.
DNA codes of different lengths.
Example 3.
Consider a cyclic code of length over ring . In , we have:
To write briefly, we identify factors by , and , respectively. The codes for are provided in Table 3. All the codes are better than the codes that appeared in [14].
Table 3.
Codes of length 27.
Example 4.
Consider a cyclic code of length over ring . In , we have
For brevity, we identify the factors by , respectively. DNA codes for are provided in Table 4. All the obtained DNA codes are better than the codes provided in [14].
Table 4.
Codes of length 45.
In particular, if , then we obtain a DNA code with parameters . Further, we list all the DNA codewords of the obtained DNA code in Table 5. Furthermore, the edit distance of the obtained DNA code is 2, given by the codewords “TCCTCCTCCTCCTCCTCCTCCTCCTCC" and “CTCCTCCTCCTCCTCCTCCTCCTCCTC".
Table 5.
Codewords of length 45 and dimension 3.
7. Conclusions
In this paper, we have studied reversible and DNA codes using the chain ring . We have defined a Gray map on and found codons corresponding to the elements of . In this way, we have obtained good DNA and reversible codes with the Hamming distances. In the future, one can work on DNA codes over a generalized structure of as well as DNA codes by using skew polynomial rings.
Author Contributions
This work is initiated by A.S. and R.K.V. under the supervision of O.P. Then we discussed it with P.S. and W.C. to reach the final version. All authors have read and agreed to the published version of the manuscript.
Funding
This research received no external funding for APC. Financial support for this work is properly acknowledged in the acknowledgement section.
Data Availability Statement
The data that support the findings of this study are available from the corresponding author upon reasonable request.
Acknowledgments
The first and second authors are thankful to the DST and the CSIR, Govt. of India, for financial support under CRG/2020/005927, vide Diary No. SERB/F/6780/ 2020-2021 dated 31 December 2020 and under File No. 09/1023(0027)/2019- EMR-1, respectively. Furthermore, we thank the Indian Institute of Technology Patna for providing research facilities.
Conflicts of Interest
The authors declare that there is no conflict of interest regarding the publication of this manuscript.
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