Yuhani Yusof

An Extension of First Order Limit Language

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.

Some Relations Between Two Stages DNA Splicing Languages

A new symbolization of Yusof-Goode (Y-G) rule, which is associated with Y-G splicing system, was introduced by Yusof in 2012 under the framework of formal language theory. The purpose of this investigation is to present the biological process of DNA splicing in a translucent way. In this study, two stages splicing languages are introduced based on Y-G approach and some relations between stage one and stage two splicing languages are presented, given as theorems. Additionally, the existing relations between two stages splicing languages based on crossings and contexts of restriction enzymes factors with respect to two initial strings (having two cutting sites) and two rules are presented as subset.

An Extension of DNA Splicing System

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 SkH systems. Also, counterexamples are given to illustrate relationships between these splicing system classes.

Some sufficient conditions for persistency and permanency of two stages DNA splicing languages via Yusof-Goode approach

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.

Hierarchy of certain types of DNA splicing systems

A Head splicing system (H-system)consists of a finite set of strings (words) written over a finite alphabet, along with a finite set of rules that acts on the strings by iterated cutting and pasting to create a splicing language. Any interpretation that is aligned with Tom Heads original idea is one in which the strings represent double-stranded deoxyribonucleic acid (dsDNA) and the rules represent the cutting and pasting action of restriction enzymes and ligase, respectively. A new way of writing the rule sets is adopted so as to make the biological interpretation transparent. This approach is used in a formal language- theoretic analysis of the hierarchy of certain classes of splicing systems, namely simple, semi-simple and semi-null splicing systems. The relations between such systems and their associated languages are given as theorems, corollaries and counterexamples.

Compatible pair of nontrivial actions for some cyclic groups of 2-power order

Compatible actions play a very important verification before the nonabelian tensor product can be computed. This paper gives the some exact number of compatible pairs of actions for some cyclic groups of 2-power order. Some necessary and sufficient numbers of theoretical conditions for a pair of cyclic groups of 2-power order with nontrivial actions which act compatibly on each other are used to investigate some properties in order to find the exact number of compatible pairs of actions. Algorithms in Groups, Algorithms and Programming (GAP) software are used to create more examples on selected cases. New results on compatible pair of nontrivial actions of order two and four for cyclic groups of 2-power order are presented in this paper.

Second Order Limit Language in Variants of Splicing System

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.

An analysis of four variants of splicing system

The theoretical development of splicing system has led to the formulation of new extension of splicing system, namely Yusof-Goode (Y-G) splicing system. This Y-G splicing system, which is associated with Y-G splicing rule, is introduced to show the transparent biological process of DNA splicing. In this paper, a theoretical analysis has been carried out to investigate the similarities and differences between Y-G splicing system with the existing splicing systems namely, Head, Paun and Pixton splicing system in biological point of view.

SOME CHARACTERIZATIONS IN SPLICING SYSTEMS

The splitting and recombinant of deoxyribonucleic acid or DNA by specified enzymes using concepts in Formal Language Theory was first mathematically modeled by Head in 1987. This splicing system, S can be presented as a set of initial string I over an alphabet A that acts upon 5′ or 3′ overhangs of restriction enzymes and can be simply viewed as S = (A, I, B, C). In this paper, a great interest in presenting some relations on certain types of splicing system namely null‐context, uniform, simple, semi‐simple, semi‐null and Sk based on differentiating their rules are given as proposition, corollaries and counterexamples.

Differentiating the Persistency and Permanency of Some Two Stages DNA Splicing Language via Yusof-Goode (Y-G) Approach

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 non-permanency of two stages DNA splicing language.