An analysis of four variants of splicing system

Yusof, Yudariah Mohammad; Sarmin, Nor Haniza; Fong, Wan Heng; Goode, T. Elizabeth; Ahmad, Muhammad Azrin

doi:10.1063/1.4801223

Cited by 8 publications

(5 citation statements)

References 5 publications

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“…Motivated by the concept from the process of recombinant DNA in Head's splicing model, variants of splicing models had been studied. For instance, Paun [6], Pixton [7], Goode-Pixton [8] and Yusof-Goode [9] splicing systems had been introduced with different notations of rule. There are different types of splicing languages such as simple [10], limit [8], second order, single and two stage splicing language which can be generated by different splicing models.…”

Section: Introductionmentioning

confidence: 99%

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

2019

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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.

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Section: Introductionmentioning

confidence: 99%

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

2019

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“…Throughout the years, notations in Head's splicing system have been extended and variants of splicing models have been developed namely Paun [9], Pixton [10], Goode-Pixton [11] and Yusof-Goode [12] splicing systems. The variants of splicing systems resulted in many types of splicing languages.…”

Section: Introductionmentioning

confidence: 99%

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

Ismail¹,

Fong²,

Sarmin³

2019

IJEAT

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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.

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“…Over the years, several models had been extended and developed like Paun [7], Pixton [8], and Yusof-Goode [9] splicing systems. Besides that, Laun [10] also developed a new model of splicing system known as Goode-Pixton splicing system.…”

Section: Introductionmentioning

confidence: 99%

“…Morever, a new extension of splicing systems known as a simple splicing system had also been introduced [10]. The comparison between Head's and these splicing models was studied in [9].…”

Section: Introductionmentioning

confidence: 99%

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

2019

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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.

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An analysis of four variants of splicing system

Cited by 8 publications

References 5 publications

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

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

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

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

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