Insertion-deletion System Research Articles

On the generative capacity of matrix insertion-deletion systems of small sum-norm

A matrix insertion-deletion system (or matrix ins-del system) is described by a set of insertion-deletion rules presented in matrix form, which demands all rules of a matrix to be applied in the given order. These systems were introduced to model very simplistic fragments of sequential programs based on insertion and deletion as elementary operations as can be found in biocomputing. We are investigating such systems with limited resources as formalized in descriptional complexity. A traditional descriptional complexity measure of such a matrix ins-del system is its size s=(k;n,i',i'';m,j',j''), where the parameters from left to right represent the maximal matrix length, maximal insertion string length, maximal length of left contexts in insertion rules, maximal length of right contexts in insertion rules; the last three are deletion counterparts of the previous three parameters. We call the sum n+i'+i''+m+j'+j'' the sum-norm of s. We show that matrix ins-del systems of sum-norm 4 and sizes (3; 1, 0, 0; 1, 2, 0), (3; 1, 0, 0; 1, 0, 2), (2; 1, 2, 0; 1, 0, 0), (2; 1, 0, 2; 1, 0, 0), and (2; 1, 1, 1; 1, 0, 0) describe the recursively enumerable languages. Moreover, matrix ins-del systems of sizes (3; 1, 1, 0; 1, 0, 0), (3; 1, 0, 1; 1, 0, 0), (2; 2, 1, 0; 1, 0, 0) and (2; 2, 0, 1; 1, 0, 0) can describe at least the regular closure of the linear languages. In fact, we show that if a matrix ins-del system of size s can describe the class of linear languages mathrm {LIN}, then without any additional resources, matrix ins-del systems of size s also describe the regular closure of mathrm {LIN}. Finally, we prove that matrix ins-del systems of sizes (2; 1, 1, 0; 1, 1, 0) and (2; 1, 0, 1; 1, 0, 1) can describe at least the regular languages.

Closure properties of bonded sequential insertion-deletion systems

Through the years, formal language theory has evolved through continual interdisciplinary work in theoretical computer science, discrete mathematics and molecular biology. The combination of these areas resulted in the birth of DNA computing. Here, language generating devices that usually considered any set of letters have taken on extra restrictions or modified constructs to simulate the behavior of recombinant DNA. A type of these devices is an insertion-deletion system, where the operations of insertion and deletion of a word have been combined in a single construct. Upon appending integers to both sides of the letters in a word, bonded insertion-deletion systems were introduced to accurately depict chemical bonds in chemical compounds. Previously, it has been shown that bonded sequential insertion-deletion systems could generate up to recursively enumerable languages. However, the closure properties of these systems have yet to be determined. In this paper, it is shown that bonded sequential insertion-deletion systems are closed under union, concatenation, concatenation closure, λ-free concatenation closure, substitution and intersection with regular languages. Hence, the family of languages generated by bonded sequential insertion-deletion systems is shown to be a full abstract family of languages.

Pattern Based Matrix Insertion Deletion System for Efficient Bio Molecular Computing System

The problem of bio molecular computing has been well studied and there are number of approaches discussed for the detection of false gene sequences. However, they suffer to achieve higher performance in the detection of false sequences. To improve the performance of detection of fake molecular patterns, an pattern based approach is discussed in this paper. As of the biomolecular strings a set of patterns, the method first identifies the list of sequences available and based on the set of patterns being maintained, the method identifies the list of patterns present in the gene sequence. Based on the sequences, the method identifies the incomplete and fake sequences and performs insertion and deletion using matrix operations. The method maintains number of patterns for the matrix insertion and deletion operation. For each pattern available, the method compute the bio molecular sequence weight. Finally a single sequence has been selected and based on the selected pattern, the method performs insertion and deletion operation. The proposed method produces efficient results on the detection as well as correction.

On path-controlled insertion–deletion systems

A graph-controlled insertion–deletion system is a regulated extension of an insertion–deletion system. It has several components and each component contains some insertion–deletion rules. These components are the vertices of a directed control graph. A transition is performed by any applicable rule in the current component on a string and the resultant string is then moved to the target component specified in the rule. This also describes the arcs of the control graph. Starting from an axiom in the initial component, strings thus move through the control graph. The language of the system is the set of all terminal strings collected in the final component. In this paper, we investigate a variant of the main question in this area: which combinations of size parameters (the maximum number of components, the maximal length of the insertion string, the maximal length of the left context for insertion, the maximal length of the right context for insertion; plus three similar restrictions with respect to deletion) are sufficient to maintain computational completeness of such restricted systems under the additional restriction that the (undirected) control graph is a path? Notice that these results also bear consequences for the domain of insertion–deletion P systems, improving on a number of previous results from the literature, concerning in particular the number of components (membranes) that are necessary for computational completeness results.

On describing the regular closure of the linear languages with graph-controlled insertion-deletion systems

A graph-controlled insertion-deletion (GCID) system has several components and each component contains some insertion-deletion rules. A transition is performed by any applicable rule in the current component on a string and the resultant string is then moved to the target component specified in the rule. The language of the system is the set of all terminal strings collected in the final component. When resources are very limited (especially, when deletion is demanded to be context-free and insertion to be one-sided only), then GCID systems are not known to describe the class of recursively enumerable languages. Hence, it becomes interesting to explore the descriptional complexity of such GCID systems of small sizes with respect to language classes below RE and even below CF. To this end, we consider so-called closure classes of linear languages defined over the operations concatenation, Kleene star and union. We show that whenever GCID systems (with certain syntactical restrictions) describe all linear languages (LIN) with t components, we can extend this to GCID systems with just one more component to describe, for instance, the concatenation of two languages from the language family that can be described as the Kleene closure of linear languages. With further addition of one more component, we can extend the construction to GCID systems that describe the regular closure of LIN.

On the computational completeness of graph-controlled insertion–deletion systems with binary sizes

A graph-controlled insertion–deletion (GCID) system is a regulated extension of an insertion–deletion system. Such a system has several components and each component has some insertion–deletion rules. The transition is performed by any applicable rule in the current component on a string and the resultant string is then moved to the target component specified in the rule. The language of the system is the set of all terminal strings collected in the final component. The parameters in the size (k;n,i′,i″;m,j′,j″) of a GCID system denote (from left to right) the maximum number of components, the maximal length of the insertion string, the maximal length of the left context for insertion, the maximal length of the right context for insertion; the last three parameters follow a similar representation with respect to deletion.In this paper, we discuss the computational completeness of the families of GCID systems of size (k;1,i′,i″;1,j′,j″) with k∈{3,5} and for (nearly) all values of i′,i″j′,j″∈{0,1}. All proofs are based on the simulation of type-0 grammars given in Special Geffert Normal Form (SGNF). The novelty in our proof presentation is that the context-free and the non-context-free rules of the given SGNF grammar are simulated by GCID systems of different sizes and finally we combine them by stitching and overlaying to characterize the recursive enumerable languages. This proof presentation greatly simplifies and unifies the proof of such characterization results. We also connect some of the obtained GCID simulations to the domain of insertion–deletion P systems.

On Succinct Description of Certain Context-Free Languages by Ins-Del and Matrix Ins-Del Systems

In this paper, we introduce some basic measures for insertion-deletion system and matrix insertion-deletion system. These measures are based on the number of variables, the number of productions and the number of symbols in a grammar. We show that with respect to these measures, both the systems are more succinct over context-free grammars in representing certain families of context-free languages.

Modelling DNA and RNA secondary structures using matrix insertion–deletion systems

Abstract Insertion and deletion are operations that occur commonly in DNA processing and RNA editing. Since biological macromolecules can be viewed as symbols, gene sequences can be represented as strings and structures can be interpreted as languages. This suggests that the bio-molecular structures that occur at different levels can be theoretically studied by formal languages. In the literature, there is no unique grammar formalism that captures various bio-molecular structures. To overcome this deficiency, in this paper, we introduce a simple grammar model called the matrix insertion–deletion system, and using it we model several bio-molecular structures that occur at the intramolecular, intermolecular and RNA secondary levels.

Minimizing of the only-insertion insdel systems

A more recent branch of natural computing is DNA computing. At the theoretical level, DNA computing is powerful. This is due to the fact that DNA structure and processing suggest a series of new data structures and operations, and to the fact of the massive parallelism. The insertion-deletion system (insdel system) is a DNA computing model based on two genetic operations: insertion and deletion which, working together, are very powerful, leading to characterizations of recursively enumerable languages. When designing an insdel computer, it is natural to try to keep the underlying model as simple as possible. One idea is to use either only insertion operations or only deletion operations. By helping with a weak coding and a morphism, the family INS 4 7 DEL 0 0 is equal to the family ofrecursively enumerable languages. It is an open problem proposed by Martin-Videet al. on whether or not the parameters 4 and 7 appearing here can be replaced by smaller numbers. In this paper, our positive answer to this question is that INS 2 4 DEL 0 0 can also play the same role as insertion and deletion. We suppose that the 1NS 2 4 DEL 0 0 may be the least only-insertion insdel system in this situation. We will give some reasons supporting this conjecture in our paper.

On Computational Power of Insertion-Deletion Systems without Using Contexts

An Insertion-Deletion system, first introduced in [1], is a theoretical computing model in the DNA computing framework based on insertion and deletion operations. When insertion and deletion operations work together, as expected, they are very powerful. In fact, it has been shown that even the very restricted Insertion-Deletion systems can characterize the class of recursively enumerable languages [1]--[4]. In this paper, we investigate the computational power of Insertion-Deletion systems and show that they preserve the computational universality without using contexts.