Some restrictions on the existence of second order limit language (original) (raw)
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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.
Second order limit language in variants of splicing system
2014
The cutting and pasting processes that occur in DNA molecules have led to the formulation of splicing system. Since then, there are few models used to model the splicing system. The splicing language, which is the product of splicing system, can be categorized into two, namely the adult and limit language. In this research, limit language is extended to the second order limit language. Few problems are approached which lead to the formation of second order limit language which is then analyzed using various types of splicing system.
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.
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.
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...
Journal of Physics: Conference Series, 2017
Predicting the existence of restriction enzymes sequences on the recombinant DNA fragments, after accomplishing the manipulating reaction, via mathematical approach is considered as a convenient way in terms of DNA recombination. In terms of mathematics, for this characteristic of the recombinant DNA strands, which involve the recognition sites of restriction enzymes, is called persistent and permanent. Normally differentiating the persistency and permanency of two stages recombinant DNA strands using wet-lab experiment is expensive and time-consuming due to running the experiment at two stages as well as adding more restriction enzymes on the reaction. Therefore, in this research, by using Yusof-Goode (Y-G) model the difference between persistent and permanent splicing language of some two stages is investigated. Two theorems were provided, which show the persistency and nonpermanency of two stages DNA splicing language.
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...
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...
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.
Jurnal Teknologi, 2015
The notation of representing restriction enzymes in the form of double-triple in order to formulate Yusof-Goode (Y-G) splicing system was mathematically proposed by Yusof in 2012. The aim of introducing Y-G splicing system was to study the process of recombinant deoxyribonucleic acid or DNA strand in a translucent way. In real situation, when the recombination action occurs, the recombinant DNA strands which will arise often contain the patterns of the restriction enzymes. Persistency and permanency are two properties of splicing system, which show whether the recombinant DNA strands will be split by the existence of restrictions enzymes or not if the reaction goes to the second stage. In this research, the persistency and permanency of two stages splicing languages according to the number of cutting sites of initial strings as well as crossing sites and context factors of splicing rules are investigated. Therefore, a Y-G splicing system consisting of two initial strings (with two c...