Second order limit language in variants of splicing system (original) (raw)
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On the new relation of second order limit language and other different types of splicing system
PROCEEDINGS OF THE 27TH NATIONAL SYMPOSIUM ON MATHEMATICAL SCIENCES (SKSM27)
Mathematical modelling of splicing system has been introduced to initiate a linkage between the study of informational macromolecules that includes DNA and formal language theory. The ability to present the nitrogenous base which is a component in a nucleotide of DNA, as a series of alphabet, ignites this interdisciplinary study. Over the years, researchers have developed models to match their need. In addition, product of splicing system is called splicing language. Through some development, second order limit language is derived from other type of languages known as limit language. Its existence and characteristics have been vastly discussed. Beside, some types of splicing system can produce second order limit language. In this research, the characteristics of varieties of splicing system are studied and their relations with second order limit language are established.
Jurnal Teknologi, 2014
DNA splicing process is a study on the recombinant behavior of double-stranded DNA molecules with the existence of restriction enzyme and ligase. Head introduced the first mathematical model of splicing systems by using the relation of informational macromolecules and formal language theory. In addition, a few laboratory experiments have been conducted in order to verify certain types of splicing language called inert/adult, transient and limit language. Previously, researchers have focused on those types of splicing languages. Recently, an extension of limit languages namely second order limit language has been introduced. In this paper, the difference between second order limit languages and non-second order limit languages is depicted in some examples. Then, the formations of second order limit language in Yusof-Goode splicing system are investigated.
Biomolecular Aspects of Second Order Limit Language
Malaysian Journal of Fundamental and Applied Sciences, 2018
The study on the recombinant behavior of double-stranded DNA molecules has led to the mathematical modelling of DNA splicing system. The interdisciplinary study is founded from the knowledge of informational macromolecules and formal language theory. A splicing language is resulted from a splicing system. Recently, second order limit language, a type of the splicing language, has been extensively explored. Before this, several types of splicing languages have been experimentally proven. Therefore, in this paper, a laboratory experiment was conducted to validate the existence of a second order limit language. To accomplish it, an initial strand of double-stranded DNA, amplified from bacteriophage lambda, was generated through polymerase chain reaction to generate thousands of copies of double-stranded DNA molecules. A restriction enzyme and ligase were added to the solution to complete the reaction. The reaction mixture was then subjected to polyacrylamide gel electrophoresis to sepa...
Persistent and Permanent Point of Views of Two Stages DNA Splicing Languages
Yusof-Goode (Y-G) splicing system was formulated by Yusof in 2012 to present the existence relation between formal language theory and molecular biology in a convenient approach. In terms of biology, the recombinant deoxyribonucleic acid (DNA) molecules can often be split with the existence of actual restriction enzymes. For this property of the recombinant DNA strands is called persistent. Therefore, determining the persistency of the hybrid templets of DNA strands, after acting restriction enzymes on the initial DNA strands, by providing mathematical proof is considered as a new contribution in the areas of DNA molecular. In this work, the persistent and permanent aspects of two stages splicing languages are investigated and discussed via Y-G approach. This investigation focuses on number of cutting sites in initial strings as well as sequences factors of splicing rules. Accordingly, the persistency and permanency of the above splicing languages with respect to two initial strings...
Some restrictions on the existence of second order limit language
2015
The cut and paste phenomenon on DNA molecules with the presence of restriction enzyme and appropriate ligase has led to the formalism of mathematical modelling of splicing system. A type of splicing system named Yusof-Goode splicing system is used to present the transparent behaviour of the DNA splicing process. The limit language that is defined as the leftover molecules after the system reaches its equilibrium point has been extended to a second order limit language. The non-existence of the second order limit language biologically has lead to this study by using mathematical approach. In this paper, the factors that restrict the formation of the second order limit language are discussed and are presented as lemmas and theorem using Y-G approach. In addition, the discussion focuses on Yusof-Goode splicing system with at most two initial strings and two rules with one cutting site and palindromic crossing site and recognition sites.
Second Order Limit Language Associated with Two Rules
The concepts of splicing system involve the study of cut and paste phenomenon of deoxyribonucleic acid (DNA). The splicing language, which is resulted from a splicing system, can be classified as inert persistent language, active persistent language and limit language. As one of the types of splicing language, limit language can biologically be referred as the remaining molecule after the process has attained its equilibrium state. In this paper, the existence of second order limit language is explored strictly using at most two initial strings and two rules. In addition, the actual biological examples are presented. By using the Y-G splicing system, the results obtained are then used to prove the existence of second order limit language in few classes of Y-G splicing system.
2014
Splicing system that was first introduced by Head makes a connection between field of formal language theory and molecular biology. This system modeled the biological process of splitting and ligating on double stranded deoxyribonucleic acid (DNA) molecules under effect of restriction enzymes and appropriate ligase. In this paper, the concept of two stages DNA splicing languages is introduced. Some sufficient conditions for persistency and permanency of the above DNA splicing languages focusing on two rules and two initial strings will be investigated by usingYusof-Good (Y-G) approach.
An extension of first order limit language
2014
The study on cutting and pasting of DNA molecules under the framework of Formal Language Theory has led to the mathematical modelling of splicing system. The output of splicing system is the splicing language which can be categorized into three types: adult or inert persistent, transient and limit language. In the biological point of view, limit language is predicted to appear after the reaction of DNA molecules and enzyme with the existence of appropriate ligase reached the equilibrium state. In this research, the second order limit language is investigated. It is defined as the distinct language after splicing occurs among the resulting splicing language of the first order splicing language. Besides that, the characteristics of second order limit language are observed based on the properties of the crossing sites of the rules such as left or right context and palindromic via Y-G approach. The results lead to some examples and theorems which are presented in this paper.
Modelling the Behaviour of Single Stage Splicing Language: A Yusof Goode Computational Approach
Jurnal Teknologi, 2015
Yusof-Goode (Y-G) splicing system is a formal characterization of the generative capacity of specified enzymatic activities acting on DNA molecules with new extension symbolization of representing rule. The output of Y-G splicing system can be categorized into three types of single stage splicing language namely active persistent, transient and inert persistent language. It is both money and time consuming to conduct laboratory experiments to determine the behaviour of splicing language. Hence, research has been conducted to predict the characteristic of single stage splicing language based on limit adjacency matrix computational modelling in order to optimize time and money. The utilization of software programming has been developed through Visual Basic Software for scientists to determine the behaviour of single stage splicing language as well as the number types of resulted DNA molecules restricted to at most two strings and two rules with one cutting site. The output from the pr...
Lecture Notes in Computer Science, 2003
We consider the result of a wet splicing procedure after the reaction has run to its completion, or limit, and we try to describe the molecules that will be present at this final stage. In language theoretic terms the splicing procedure is modeled as an H system, and the molecules that we want to consider correspond to a subset of the splicing language which we call the limit language. We give a number of examples, including one based on differential equations, and we propose a definition for the limit language. With this definition we prove that a language is regular if and only if it is the limit language of a reflexive and symmetric splicing system.