Abstract
Let be a non-chain ring of characteristic 4, where and . In this article, we discuss reversible cyclic codes of odd lengths over the ring . We construct bijections between the elements of the ring and DNA- bases for k = 1, 2 in such a manner that the reversibility problem is solved. Employing these bijections, reversible complement cyclic codes of odd lengths are generated. Furthermore, we construct a Gray map and as an application of the Gray map Φ, we obtain the GC-content of cyclic codes of arbitrary odd length over the ring . Meanwhile, we provide some examples of reversible cyclic codes of odd lengths over the ring for different values of k, and also obtain the Lee distances of these codes.
1. Introduction
Identifying elements of an algebraic structure (fields, rings, etc.) having cardinality , where with DNA-k bases is a fascinating problem. Suppose an algebraic structure has only four elements and if we identify these elements with the four nucleotides , then any reversible code over the algebraic structure X will always corresponds to a reversible DNA code. On the other hand, this is not true, if , where k>1 then a reversibility problem occur. In order to clarify the reversibility problem we present an example. Suppose is a codeword of length 4 over X. We identify code alphabets of the codeword β with DNA double pairs as follows: , , , and . Therefore, corresponding DNA sequence to the codeword β is AAGACTAT. The reverse codeword of β is given by and corresponding DNA sequence to is ATCTGAAA. One can verify that the DNA sequence ATCTGAAA is not the reverse of AAGACTAT. In fact the reverse of the DNA sequence AAGACTAT is TATCAGAA. This reversibility problem was invented by Oztas and Siap [Citation1], where the authors first made use of lifted polynomials over to solve this problem.
Many researchers solved this reversibility problem by using different techniques. For example, Gursoy et al. [Citation2] make use of skew cyclic codes over a non-chain ring to solve the reversibility problem. Oztas et al. [Citation3] solved the reversibility problem that occur in DNA k-bases using the coterm polynomials. Further, Oztas and Siap [Citation4] obtained the generalization of lifted polynomials and solved this reversibility problem. Moreover, Ashraf et al. [Citation5] employed reversible cyclic codes over a non-chain ring to solve this reversibility problem.
The interest on DNA computing was initiated by Adleman [Citation6]. In Adleman [Citation6] performed an experiment involving the use of DNA molecules based on the Watson–Crick complement (WCC) model of a DNA strand in solving the famous directed salesman problem. Later on, a molecular program is provided by Adlemen et al. [Citation7] for breaking the symmetric cryptographic algorithm (DES). Additionally, it was demonstrated in [Citation8] that DNA molecules can be employed as a storage media. Multiple theories are necessary for developing DNA sequences that satisfy certain constraints. We call a given sequence , a quaternary n-sequence or a DNA sequence if , where . According to the Watson-Crick complement rule, a DNA sequence combined with its complement (reversible) forms a helix. The Complement of T is A (and vice versa), and the complement of G is C (and vice versa). We denote by , , , , where , , , and are the complements of C, G, A and T respectively. For example, the Watson-Crick complement of . A DNA code of length n is the collection of DNA sequences of length n where each sequence occurs with its reverse complement sequence i.e. , where is the reverse complement of .
The ability to construct DNA codes that fulfill particular constraints is of utmost importance in various domains, including biotechnology and security. These applications encompass a range of areas, such as DNA computing, DNA cryptography, and DNA steganography (see [Citation7, Citation9] and references therein). A cyclic DNA code always satisfies the Hamming distance constraint and it may satisfy the other three constraints listed below
The Hamming constraint: If , where and for some Hamming distance d.
The Reverse constraint: If , where for some Hamming distance d, and is the reverse of .
The Reverse-complement constraint: If , where for some Hamming distance d, and is the reverse complement of .
The Fixed GC-content constraint: If any codeword contains the same number of G and C.
The objective of the first three constraints is to reduce the probability of non-specific hybridization. The fixed GC-content constraint is used to obtain similar melting temperatures.
Reversible codes have versatile applications in the design of DNA codes as well as data storage and retrieval systems. In [Citation10], the author started the study of reversible codes and provided conditions for a given cyclic code over a finite field to be reversible. In [Citation11], a relation between the minimum distance of certain reversible cyclic codes and BCH bounds is obtained. In addition to the above studies, the authors in [Citation12] constructed reversible cyclic codes over . Later on, Abualrab [Citation13] obtained quaternary reversible cyclic codes. In [Citation14–16] the authors obtained criteria for negacyclic, constacyclic and quasi-cyclic codes to be reversible respectively. Moreover, in [Citation17] the authors provided a survey of DNA codes over finite rings. For the intensive study of reversible cyclic codes over different algebraic structures, we refer to the readers (see [Citation18–27] and references therein). Meanwhile, Siap et al. [Citation28] obtained cyclic DNA codes over the ring based on the deletion distance. Further, Yildiz and Siap [Citation29] constructed cyclic DNA codes of odd length satisfying the Hamming distance constraint over the ring . Later on, Dinh et al. [Citation30] obtained cyclic DNA codes over the ring , where . Moreover, Guenda and Gulliver [Citation31] constructed DNA codes over the ring , satisfying the reverse constraint, the reverse-complement constraint and the GC-content constraint.
Inspired by these studies, in the present article we construct reversible cyclic codes of any odd length over the ring . We construct bijections namely () between the elements of the ring and DNA- bases in such a manner that the reversibility problem has been solved for every k. Furthermore, as an application of these bijections reversible complement codes of any odd length are generated over the ring . Moreover, we study the GC-content of DNA codes over the ring . In addition, some examples of reversible code are constructed.
The organization of the present article is as follows: In Section 2, we discuss some basic definitions. Section 3 comprises structure of cyclic codes of any odd length over the ring . In Section 4, we provide a necessary and sufficient condition for a given cyclic code over the ring to be reversible. Also, we construct bijections for k = 1, 2 (see Tables and ) in such a manner that the reversibility problem has been solved. Similarly, one can construct for rest of the values of k, with the aforementioned properties. Moreover, by utilizing these bijections reversible-complement cyclic codes of odd lengths are generated. In Section 5, we provide a Gray map and discuss the GC-content in terms of the Gray images. Finally, in Section 6 we provide some examples of reversible cyclic codes of different odd lengths over the ring .
2. Preliminaries
We begin this section by characterizing the ring . Let be a finite ring. Here, we make use of results presented in (see [Citation32–35]), where the authors obtained linear codes over the ring , for k = 1, 2. Suppose , where B is a subset of the set . It is worth to notice that every element of the ring can be written uniquely as , where and is any subset of the set . In particular we assume that . Also, observe that for any subsets we have and therefore we obtain
Lemma 2.1
The ring has characteristic 4 and cardinality .
Proof.
Since the coefficients of are the members of , it follows directly that characteristic of the ring is 4. Also, observe that for any given element there are four choices for each and subsets of the set . This shows that cardinality of the ring is .
An element e is called an idempotent element if . Suppose are two idempotent elements if , then and are said to be orthogonal idempotent. Now we list all orthogonal idempotent elements of the ring in Table . Kumar and Singh [Citation26], Li et al. [Citation35] and Bustomi [Citation36] obtained all orthogonal idempotent elements over the ring for k = 1, k = 2 and k = 3 respectively. Here, we use the same technique which is presented in [Citation26, Citation35, Citation36] to count all orthogonal idempotents in the ring .
By observing Table , the total number of orthogonal idempotent elements in the ring are . We denote all idempotent elements by . All idempotent elements are also pairwise orthogonal, since , for and for and also we have . Hence, by Chinese remainder theorem we obtain Recall that a linear code of length n over is an -submodule of and members of are known as codewords. A cyclic shift on is a permutation σ given by A code is said to be a cyclic code if it is invariant under σ. The inner-product of two given n-tuples , is defined as , a and b are said to be orthogonal if . For a given linear code , we define the dual code over the ring in the following manner One can verify that is a linear code over the ring of same length as . In addition, If then a linear code is said to be self-orthogonal and if then we call a linear code is self-dual. The reciprocal polynomial of a given polynomial is defined as . It is worth to mention that and if , then . A given polynomial is said to be self-reciprocal if .
We need the following result which provides the criteria for obtaining the reciprocal of sum and product of polynomials.
Lemma 2.2
[Citation13]
Suppose and are two polynomials over the ring , where . Then the following statements hold:
(1) | , | ||||
(2) | , provided . |
3. Structure of cyclic codes over
In this section, the structure of cyclic codes over the ring is conferred. For obtaining the generating set of a cyclic code over the ring , we make use of cyclic codes over the ring . In [Citation37], the authors obtained non-linear codes over the ring as Gray images of binary codes. Many researchers have obtained the structure of cyclic codes over the ring . For example, in [Citation13] the author provided generating set of cyclic codes over the ring of arbitrary length. Similarly, Pless and Qian [Citation38] obtained a different generating set for cyclic codes of odd lengths over the ring . In the present article, we use generating set given in [Citation38]. Therefore, we have following result.
Theorem 3.1
[Citation38]
Suppose is a cyclic code of odd length n over the ring . Then is given by , where , and are monic polynomials such that . Moreover, is of the type .
We obtain the decomposition of a linear code over the ring in terms of the linear codes , where each is given as follows: It is easy to observe that each is a linear code over the ring and therefore can be uniquely decomposed as (1) (1) Now, we present the following results which are helpful in describing the structure of linear codes over the ring .
Theorem 3.2
Let be a linear code of length n over the ring . Then , where each is a linear code over , and the direct sum decomposition is unique. Moreover, the dual code of is given by , where is the dual code of the linear code .
Proof.
Proof of the first part follows directly from the Decomposition (Equation1(1) (1) ). For the dual code, suppose that . Take any and , where , and , . Now, consider , we must have . Hence, we obtain . For the converse part, notice that is a Frobenius ring. Thus . Therefore, we obtain .
Corollary 3.3
Let be a linear code over the ring given by . Then is a self-orthogonal if and only if each is self-orthogonal over . Furthermore, is a self-dual if and only if each is self-dual over .
Proof.
The result directly follows from Theorem 3.2.
Theorem 3.4
Let be a linear code of length n given by . Then is a cyclic code over the ring if and only if each is a cyclic code over the ring .
The following theorem provides the generating set of a given cyclic code of any odd length.
Theorem 3.5
Let be a cyclic code of odd length n over the ring . Then is given by where ; and .
Proof.
The above result is a direct consequence of Theorem 3.1.
4. Reversible-complement DNA codes
In this section, we discuss reversibility of cyclic codes of any odd length over the ring . We provide a necessary and sufficient condition for a given cyclic code of any odd length over the ring to be reversible. Moreover, in this section we provide lemmas which are useful in solving the reversibility problem. Further, we discuss reversible-complement codes over the ring .
Definition 4.1
A block code will be called reversible if the block of digits formed by reversing the order of the digits in a codeword is always another codeword in the same code.
In [Citation10], the author obtained a condition for a given cyclic code over a finite field to be reversible.
Theorem 4.2
Suppose is a cyclic code over given by . Then is reversible if and only if .
The following result provides a necessary and sufficient condition for the reversibility of cyclic codes of odd lengths over the ring in terms of their generating polynomials.
Theorem 4.3
Let be a cyclic code of odd length n over the ring given by where ; and . Then is a reversible cyclic code over the ring if and only if each and are self-reciprocal polynomials.
Proof.
Suppose is a reversible cyclic code over the ring .Suppose on contrary, the polynomial is not self-reciprocal i.e. . Suppose . Then there exist polynomials , such that and . Let be the set of all orthogonal idempotents. Since is a reversible cyclic code over the ring , for all . This contradicts the fact that is a minimal degree generating polynomial of . Therefore, we can conclude that . Thus, each is a self-reciprocal polynomial. Similarly, one can prove for .
Conversely, assume that and are self-reciprocal polynomials i.e. and , where . Let be any element. Then there exist polynomials , , over the ring such that The reciprocal polynomial of the polynomial can be obtained using Lemma 2.2. Since and , where , we get Therefore, we obtain . Hence, is a reversible cyclic code over the ring .
Example 4.4
Suppose k = 1, consider the ring , where . We factorize the polynomial over the ring as follows: . We can verify that and both are self-reciprocal polynomials over the ring . Several reversible cyclic codes with their Gray images are listed in Table .
The following result provides the reversibility of a given cyclic code in terms of .
Theorem 4.5
Suppose is a cyclic code of odd length n over the ring given by . Then is a reversible cyclic code over the ring if and only if each is a reversible cyclic code over .
Proof.
Assume that is a reversible cyclic code of length n over the ring . Let be any element such that , where . Now, the reverse of x is given by . Suppose , where . Then, . Therefore, , . Thus each is a reversible cyclic code.
Conversely, assume that each is a reversible cyclic code over the ring . Let be any element such that , where . The reverse of x is given by . Since , . Therefore, we can conclude that is a reversible cyclic code.
Our current focus is on the reversible-complement cyclic codes characterized by odd lengths. We will establish a condition that is both necessary and sufficient for a cyclic code to be categorized as a reversible-complement cyclic code over the ring . To accomplish this, we discuss the foundational concepts of complement over the ring . For every k, we denote the complement of an element by and define as: . Let , where . Then the complement of ) is defined as follows: , where denotes the complement of for , . The reverse-complement of is denoted by and is defined as: .
Recall that the Watson-Crick complement for a given DNA sequence is given by .
From Table , we notice that if is a DNA sequence corresponding to element , then corresponds to z + 2. Similarly, from Table , we notice that if is a DNA sequence corresponding to element , then corresponds to z + 2. Next we discuss the construction of two bijections and separately. Based on these constructions, one can obtain a bijection between the elements of the ring and DNA- bases, where k is any positive integer.
For k = 1
We define the complement of an element as . In general, a given DNA double pair is associated with an element such that the Watson-Crick complement corresponds to . Further, the reverse is associated with . Notice that there are four DNA double pairs namely such that the reverse of each codeword coincides with itself. These four DNA double pairs are associated with the four elements of the set , where 3b = b for all . Moreover, there are four DNA double pairs namely whose reverse coincides with their Watson-Crick complement. We associate these pairs with the four elements of the set , where 3b = b + 2 for all .
For k = 2
In general, any given DNA-4 base can be identified with an element such that the Watson-Crick complement is associated with . Moreover, the reverse is associated with . There are some special DNA sequences which are associated as follows: Consider a set . Total number of DNA-4 bases in the set P is 16. On the other hand, cardinality of the set is also 16. We identify all DNA-4 bases of the set P with the elements of the set . Furthermore, consider the following set and . There exists a subset of the ring with cardilaity 16. We associate DNA-4 bases of the set Q, with elements of the set . Rest of the DNA-4 bases are associated with the above general rule. Similarly, we can construct bijections for other values of k, where k is any positive integer.
Next we describe how these bijections are helpful in solving the reversibility problem. In this manuscript, we construct bijections ( & ) between the elements of the ring and DNA- bases (where k = 1, 2) in Tables and such that the reversibility problem is solved. Therefore, the following lemma plays a key role in solving the reversibility problem that occurred due to the DNA double pair.
Lemma 4.6
Suppose is a codeword of length n over the ring . Let be the corresponding DNA sequence to the codeword a. Then, DNA sequence corresponding to the codeword is the reverse of D i.e. .
Let be a codeword over the ring . According to Table , the DNA sequence corresponding to θ is AGTTCATG. Now consider the codeword . By using Table , corresponding DNA sequence to the codeword is GTACTTGA. We can verify that GTACTTGA is the reverse of AGTTCATG. Similarly for k = 2, we obtain the following result.
Lemma 4.7
Suppose is a codeword of length n over the ring . Let be the DNA sequence corresponding to the codeword a. Then, DNA sequence corresponding to the codeword is the reverse of D i.e. .
Theorem 4.8
Let be a cyclic code of odd length n over the ring given by where ; and . Then is a reversible complement cyclic code over the ring if and only if
(i) | the element , | ||||
(ii) | and are self-reciprocal polynomials. |
Proof.
Suppose is a reversible-complement cyclic code over . Assume . Since is reversible-complement, . Now, where can be identified by in .
Now, for the first condition take any . Let where , . Then the reciprocal polynomial is given by (2) (2) Let be a polynomial over . Then the reverse of is given by and the reverse-complement is given by Now multiplying both sides of the above expression by we obtain (3) (3) On adding to both sides of (Equation3(3) (3) ), we obtain (4) (4) Notice that is a reversible-complement cyclic code and condition (ii) holds, using (Equation4(4) (4) ) we obtain . Using the same argument, we must have , and hence from (Equation2(2) (2) ), we get for . Therefore, is a reversible cyclic code.
Conversely, assume that conditions (i) & (ii) are satisfied. Then, we have to show that is a reversible-complement cyclic code. Since is a reversible cyclic code, for all . Let be an arbitrary codeword. Then the reverse-complement of is given by multiplying by on both sides in the above polynomial, we obtain On adding to both sides of the above expression, we obtain Now, on simplifying the above expression we find that (5) (5) Utilizing conditions (i) and (ii) in theorem with Equation (Equation5(5) (5) ) leads to the conclusion that belongs to . Consequently, we must have is a reversible-complement cyclic code over the ring .
5. The GC–content
The thermodynamic stability of the bond formed between the complementary nucleotide bases C and G exceeds that of the bond formed between the complementary nucleotide bases A and T. Consequently, DNA sequences tend to exhibit a preference for being rich in GC content. Moreover, in DNA codes the same GC-content in every codeword ensures that the codewords have similar hybridization energy and melting temperature. This motivates to consider such DNA codes in which all codewords have the same GC-content. In this section, we construct a Gray map Φ which can be utilize to obtain the GC-content. Suppose are the nucleotides. We identify these four nucleotides with the elements of the ring as follows , , and . Note that every element can be uniquely written as where . We construct a map as follows: It is worth to notice that . Therefore, we can conclude that Φ is a Lee distance preserving map. Moreover, Φ is a –linear. Similarly, we can extend the map .
Theorem 5.1
Suppose is a linear code of length n over the ring with minimum Lee distance . Then, is a linear code of length and minimum Lee distance .
Moreover, since each element of is identified by the nucleotides , Φ can also be viewed as .
The next theorem provides the minimal generating set of a given cyclic code of odd length over the ring .
Theorem 5.2
[Citation38]
Let be a cyclic code of odd length n over the ring given by , where , and are monic polynomials such that . Then minimal generating set of is given by .
We obtain the minimal generating set for a cyclic code of odd lengths over the ring as follows:
Theorem 5.3
Let be a cyclic code of odd length n over the ring given by Then minimal generating set Γ of is given by where is the minimal generating set of .
To obtain the GC-content over the ring we use a method presented in [Citation26], where the authors obtained the GC-content over the ring for k = 1 in terms of Gray images of minimal generating set of a code over the ring . The Gray image of minimal generating set Γ is given by . The GC-content is given by the Hamming weight of 2. Therefore, the next theorem provides the GC-content.
Theorem 5.4
Suppose is a cyclic code of odd length n over the ring given by , where and . Then the GC-content over the ring is the Hamming weight enumerator of
Proof.
Since GC-content can be obtained by multiplying Gray images of minimal generating sets of cyclic code with 2, using Theorem 5.3 we obtain Therefore, the GC-content is given by the Hamming weight enumerator of
Example 5.5
Let k = 1, be the ring, where . Factorize the polynomial over the ring as follows: . Suppose is a cyclic code over the ring of length 9 given by , where , and . Therefore, by using Theorem 5.4, the GC-content of the cyclic code is given by
6. Examples
Here, we provide some examples of reversible cyclic codes of different odd lengths over the ring , for k = 1, 2. After comparing the Gray images of these reversible cyclic codes with online data available in [Citation39], we find that some reversible codes have good parameters. Moreover, we construct few reversible complement codes of different length over the ring .
Example 6.1
For k = 1 consider the ring , . We factorize the polynomial over as follows: Then various reversible cyclic codes of length 9 and their Gray images are listed in Table . Suppose be cyclic code of length 9 over the ring . It is worth to notice that . Therefore, by using Theorem 4.8, is a reversible complement code over the ring . Moreover, is a DNA code of length 18, given in Table .
Example 6.2
Consider the factorization over the ring . Let k = 1 and , where be the ring. Then we provide some reversible cyclic codes over the ring and their Gray images which are given in Table . Let be a cyclic code of length 17 over the ring . Then . Therefore, by using Theorem 4.8, will be a reversible complement code. Moreover, is a DNA code of length 34, given in Table .
Example 6.3
Suppose that k = 2, and consider the ring where , , and . We obtain the factors of the polynomial over the ring as follows: Then different reversible cyclic codes of length 25 are listed in Table .
7. Conclusion
In this article, we have identified elements of the ring with DNA- bases for k = 1, 2 in such a manner that the reversibility problem occur in DNA- bases is solved. Using this idea, one can construct bijections between the elements of the ring and DNA- bases for other choices of k. We have constructed DNA codes which satisfy the Hamming constraint, the reverse constraint and the reverse-complement constraints. We have provided a necessary and sufficient for a given cyclic code of odd length over the ring to be reversible and as an application, we have constructed some examples of reversible codes and obtained their -Gray images. Furthermore, some reversible complement codes of any odd length over the ring have been generated. We obtained the GC-content of a given cyclic code over the ring as the Gray images of the Hamming weight enumerator. For future study, it would be fascinating to construct reversible cyclic codes of even lengths over the ring .
Remark
All codes in the above examples are calculated using Magma software [Citation40].
Acknowledgments
The authors extend their gratitude to the referees for their meticulous examination of the manuscript, constructive comments, and valuable suggestions, all of which have greatly enhanced the paper's quality. Moreover, the authors extend their appreciation to Princess Nourah Bint Abdulrahman University (PNU), Riyadh, Saudi Arabia for funding this research under researchers supporting number (PNURSP2024R231).
Data availability statement
This manuscript has no associated data set.
Disclosure statement
No potential conflict of interest was reported by the author(s).
Additional information
Funding
References
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