scholarly journals Automata for DNA Splicing Languages with Palindromic and Non-Palindromic Restriction Enzymes using Grammars

MATEMATIKA ◽  
2019 ◽  
Vol 35 (4) ◽  
pp. 1-14
Author(s):  
Wan Heng Fong ◽  
Nurul Izzaty Ismail ◽  
Nor Haniza Sarmin
Keyword(s):  
Dna Sequences ◽  
Formal Language ◽  
Restriction Enzymes ◽  
Language Theory ◽  
Dna Assembly ◽  
Dna Molecules ◽  
Splicing Systems ◽  
Transition Graphs ◽  
Palindromic Sequences ◽  
Dna Splicing

In DNA splicing system, DNA molecules are cut and recombined with the presence of restriction enzymes and a ligase. The splicing system is analyzed via formal language theory where the molecules resulting from the splicing system generate a language which is called a splicing language. In nature, DNA molecules can be read in two ways; forward and backward. A sequence of string that reads the same forward and backward is known as a palindrome. Palindromic and non-palindromic sequences can also be recognized in restriction enzymes. Research on splicing languages from DNA splicing systems with palindromic and non-palindromic restriction enzymes have been done previously. This research is motivated by the problem of DNA assembly to read millions of long DNA sequences where the concepts of automata and grammars are applied in DNA splicing systems to simplify the assembly in short-read sequences. The splicing languages generated from DNA splicing systems with palindromic and nonpalindromic restriction enzymes are deduced from the grammars which are visualised as automata diagrams, and presented by transition graphs where transition labels represent the language of DNA molecules resulting from the respective DNA splicing systems.

scholarly journals Generalisations of Splicing Languages in DNA Splicing Systems Involving Two Palindromic Restriction Enzymes

2021 ◽  
Vol 17 (2) ◽  
pp. 128-138
Author(s):  
Wan Heng Fong ◽  
Nurul Izzaty Ismail ◽  
Nor Haniza Sarmin
Keyword(s):  
Restriction Enzyme ◽  
Dna Computing ◽  
Formal Language ◽  
Restriction Enzymes ◽  
Language Theory ◽  
Dna Molecules ◽  
Induction Method ◽  
Different Types ◽  
Splicing Systems ◽  
Dna Splicing

DNA splicing system is initiated by Head to mathematically model a relation between formal language theory and DNA molecules. In DNA splicing systems, DNA molecules are cut and recombined in specific ways with the existence of enzymes, which are also known as endonucleases, to produce further molecules. The resulting molecules are depicted as splicing languages by using concepts in formal languages theory. A sequence of restriction enzyme that reads the same forward and backward is called as a palindromic rule. Previously, researches on different types of splicing languages have been done. In this research, generalisations of splicing languages resulting from DNA splicing systems with non-overlapping cutting sites of two palindromic restriction enzymes are presented as theorems using the induction method. The results from this research are beneficial for researchers in the field of DNA computing since it contributes to the development of splicing languages generated from DNA splicing systems with different palindromic restriction enzymes by using these generalisations.

scholarly journals DNA Splicing Systems with at Most Two Cutting Sites of a Non-Palindromic Restriction Enzyme

MATEMATIKA ◽  
2019 ◽  
Vol 35 (2) ◽  
pp. 129-137
Author(s):  
Nurul Izzaty Ismail ◽  
Fong Wan Heng ◽  
Nor Haniza Sarmin
Keyword(s):  
Restriction Enzyme ◽  
Restriction Enzymes ◽  
Dna Molecules ◽  
Dna Molecule ◽  
Splicing Systems ◽  
Palindromic Sequences ◽  
Dna Splicing

The modelling of splicing systems is simulated by the process of cleaving and recombining DNA molecules with the presence of a ligase and restriction enzymes which are biologically called as endodeoxyribonucleases.  The molecules resulting from DNA splicing systems are known as splicing languages. Palindrome is a sequence of strings that reads the same forward and backward.  Research on generalisations of splicing languages in DNA splicing system involving palindromic sequences for restriction enzymes has been done previously. In this research, the splicing languages resulting from DNA splicing systems with one non-palindromic restriction enzyme are determined using the notation from Head splicing system.  The generalisations of splicing languages for DNA splicing systems involving one and two non-overlapping cutting sites of one non-palindromic restriction enzyme are presented in the first and second theorems, respectively, which are proved using direct and induction methods.  The result from the first theorem shows a trivial string which is the initial DNA molecule; while the second theorem determines a splicing language consisting of a set of resulting DNA molecules from the respective DNA splicing system.

scholarly journals Generalisations of DNA Splicing Systems with One Palindromic Restriction Enzyme

MATEMATIKA ◽  
2018 ◽  
Vol 34 (1) ◽  
pp. 59-71 ◽  
Author(s):  
Fong Wan Heng ◽  
Nurul Izzaty Ismail
Keyword(s):  
Restriction Enzyme ◽  
Formal Language ◽  
Restriction Enzymes ◽  
Potential Effect ◽  
Language Theory ◽  
Regular Expressions ◽  
Nitrogen Bases ◽  
Restriction Sites ◽  
Splicing Systems ◽  
Dna Splicing

In DNA splicing system, the potential effect of sets of restriction enzymes and a ligase that allow DNA molecules to be cleaved and re-associated to produce further molecules is modelled mathematically.  This modelling is done in the framework of formal language theory, in which the nitrogen bases, nucleotides and restriction sites are modelled as alphabets, strings and rules respectively.  The molecules resulting from a splicing system is depicted as the splicing language.  In this research, the splicing language resulting from DNA splicing systems with one palindromic restriction enzyme for one and two (non-overlapping) cutting sites are generalised as regular expressions.

scholarly journals Computation of Splicing Languages from DNA Splicing System Based on Sequences of Restriction Enzymes

2019 ◽  
Vol 8 (6S3) ◽  
pp. 31-42
Keyword(s):  
Restriction Enzyme ◽  
Dna Computing ◽  
Restriction Enzymes ◽  
Visual Programming ◽  
Cleavage Pattern ◽  
Dna Molecules ◽  
Splicing Systems ◽  
Dna Splicing

In DNA splicing systems, restriction enzymes and ligases cleave and recombine DNA molecules based on the cleavage pattern of the restriction enzymes. The set of molecules resulting from the splicing system depicts a splicing language. In this research, an algorithm for DNA splicing systems is developed using C++ visual programming. The splicing languages which have been characterised through some theorems based on the crossings and sequences of the restriction enzymes, are generated as the output from this computation. In order to generate the splicing languages, the algorithm detects and calculates the number of cutting sites of the restriction enzymes found in the initial molecules, determines whether the sequence of restriction enzyme is a palindrome or not, and if the restriction enzymes have the same or different crossings. The results from this research depict the splicing languages obtained from the manual computations, which contributes to the development of computational software in DNA computing.

scholarly journals Computation of splicing languages from DNA splicing system with one palindromic restriction enzyme

2018 ◽  
Vol 14 (2) ◽  
pp. 188-192
Author(s):  
Nurul Izzaty Ismail ◽  
Wan Heng Fong ◽  
Nor Haniza Sarmin
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Restriction Enzyme ◽  
Restriction Enzymes ◽  
In Vitro Experiments ◽  
Dna Molecules ◽  
C Programming ◽  
Splicing Systems ◽  
Dna Splicing

In DNA splicing system, the potential effects of sets of restriction enzymes and a ligase that allow DNA molecules to be cleaved and reassociated to produce further molecules are studied.  A splicing language depicts the molecules resulting from a splicing system.  In this research, a C++ programming code for DNA splicing system with one palindromic restriction enzyme for one and two (non-overlapping) cutting sites is developed.  A graphical user interface, GUI is then designed to allow the user to insert the initial DNA string and restriction enzymes to generate the splicing languages which are the result of the computation of the C++ programming.  This interface displays the resulting splicing languages, which depict the results from in vitro experiments of the respective splicing system.  The results from this research simplify the lenghty manual computation of the resulting splicing languages of DNA splicing systems with one palindromic restriction enzyme.   

scholarly journals On Special forms of Splicing on Arrays and Graphs

Triangle ◽  
2018 ◽  
pp. 119
Author(s):  
K. G. Subramanian ◽  
A. Roslin Sagaya Mary ◽  
P. Helen Chandra
Keyword(s):  
Dna Computing ◽  
Formal Language ◽  
Restriction Enzymes ◽  
Great Depth ◽  
Formal Language Theory ◽  
Language Theory ◽  
Dna Molecules ◽  
Higher Dimensional ◽  
Theoretical Results ◽  
Theory Extension

Tom Head (1987), in his pioneering work on formal language theory applied to DNA computing, introduced a new operation of splicing on strings, while proposing a model of certain recombination behaviour of DNA molecules under the action of restriction enzymes and ligases. Since then this operation has been studied in great depth giving rise to a number of theoretical results of great interest in formal language theory. Extension of this operation of splicing to higher dimensional structures such as circular words, arrays, trees and graphs have been proposed in the literature. Here we examine the effect of certain specific forms of the splicing operation applied to arrays and graphs.

scholarly journals THE CHARACTERIZATIONS OF DIFFERENT SPLICING SYSTEMS

2012 ◽  
Vol 09 ◽  
pp. 89-94
Author(s):  
FARIBA KARIMI ◽  
NOR HANIZA SARMIN ◽  
FONG WAN HENG
Keyword(s):  
Formal Language ◽  
Biological Process ◽  
Dna Recombination ◽  
Restriction Enzymes ◽  
Theoretical Computer Science ◽  
Language Theory ◽  
Discrete Mathematics ◽  
Theoretical Computer ◽  
Points Of View ◽  
Splicing Systems

The concept of splicing system was first introduced by Head in 1987 to model the biological process of DNA recombination mathematically. This model was made on the basis of formal language theory which is a branch of applied discrete mathematics and theoretical computer science. In fact, splicing system treats DNA molecule and the recombinant behavior by restriction enzymes and ligases in the form of words and splicing rules respectively. The notion of splicing systems was taken into account from different points of view by many mathematicians. Several modified definitions have been introduced by many researchers. In this paper, some properties of different kinds of splicing systems are presented and their relationships are investigated. Furthermore, these results are illustrated by some examples.

A New Relation of Second Order Limit Language in Simple and Semi-Simple Splicing System

2014 ◽  
Vol 71 (5) ◽  
Author(s):  
Muhammad Azrin Ahmad ◽  
Nor Haniza Sarmin ◽  
Wan Heng Fong ◽  
Yuhani Yusof
Keyword(s):  
Formal Language ◽  
Theoretical Study ◽  
Second Order ◽  
Language Theory ◽  
Biological Traits ◽  
Dna Molecules ◽  
Double Stranded Dna ◽  
New Type ◽  
Limit Language ◽  
Dna Splicing

Splicing system, which is an abstraction of operations on DNA molecules, can be modelled mathematically under the framework of formal language theory and informational macromolecules. The recombinant behavior of the set of double-stranded DNA molecules under the influence of restriction enzyme and ligase further lead to the cut and paste phenomenon in splicing system. The theoretical study of splicing language has contributed to a new type of splicing language known as a second order limit language, which is an extension of limit language. Some types of splicing system can produce second order limit language. Y-G splicing system is chosen among other models to model the DNA splicing process as this model preserves the biological traits and presents the transparent behavior of the DNA splicing process. In this paper, the relation between second order limit language with simple splicing and semi-simple splicing system are presented.

A Comparison of Second Order and Non-Second Order Limit Language Generated by Yusof-Goode Splicing System

2014 ◽  
Vol 72 (1) ◽  
Author(s):  
Muhammad Azrin Ahmad ◽  
Nor Haniza Sarmin ◽  
Wan Heng Fong ◽  
Yuhani Yusof
Keyword(s):  
Mathematical Model ◽  
Restriction Enzyme ◽  
Formal Language ◽  
Laboratory Experiments ◽  
Second Order ◽  
Language Theory ◽  
Double Stranded Dna ◽  
The Difference ◽  
Splicing Systems ◽  
Limit Language

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. 

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