Persistency and Permanency of Two Stages Splicing Languages via Yusof-Goode Approach: Two Initial Strings and Two Rules (original) (raw)
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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.
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...
The concepts of persistent and permanent in non semi-simple DNA splicing system
2014
The investigation on the behavior of deoxyribonucleic acid (DNA) splicing languages has been of interest of many biologists and mathematicians. Yusof-Goode (Y-G) splicing system has been introduced for the purpose of showing the transparent biological process of DNA splicing systems. In this paper, the approach of Y-G splicing system is applied in presenting the persistency and permanent characteristics of non semi-simple DNA splicing system of Type I and Type II.
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...
An Extension of DNA Splicing System
2011 Sixth International Conference on Bio-Inspired Computing: Theories and Applications, 2011
The first mathematical model of a splicing system that was analyzed in the framework of Formal Language Theory was developed in 1987 by Head. This model consists of a finite alphabet, a finite set of initial strings over the alphabet, and a finite set of rules that act upon the strings by iterated cutting and pasting, generating new strings. In this paper, a new notation for writing rules in a splicing system and a new extension of splicing systems is introduced in order to make the biological process transparent. These are called Yusof-Goode rules, and they are associated with Yusof-Goode splicing systems. Four different classes of splicing systems are discussed: null-context, uniform, simple and S k H systems. Also, counterexamples are given to illustrate relationships between these splicing system classes.
Modelling of Two Stages Dna Splicing Languages on De Bruijn Graph
Jurnal Teknologi, 2015
Finding the sequence of the genome from its compositions as well as a mathematical graph is the most interesting topic in a field of DNA molecular. Since lack of technology is the big obstacle that biologists are facing to read a long sequence of the genome from beginning up to the end, therefore finding the compositions of the genome having very long sequence and also its description via de Bruijn graph is challenging or even impossible. In this paper, Yusof-Goode (Y-G) approach is used to generate the DNA splicing languages based on cutting sites of initial strings (one or two cutting sites) and crossing and contexts factors of restriction enzymes. The two short sequences of DNA (8bp) and two restriction enzymes are considered to create a connection between mathematics and DNA molecular. This relation will be presented as de Bruijn graph so that every edge of the de Bruijn graph gives a k-mer composition of DNA molecule and also each path of the de Bruijn graph gives a DNA sequence and vice-versa. Besides, the persistency and permanency of two stages DNA splicing languages can be predicted using this model.
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.