Algorithms for Splicing Systems

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

Malaysian Journal of Fundamental and Applied Sciences ◽

10.11113/mjfas.v14n2.879 ◽

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.

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Group II intron architecture and its implications for the development of eukaryotic splicing systems

The FASEB Journal ◽

10.1096/fasebj.26.1_supplement.217.3 ◽

2012 ◽

Vol 26 (S1) ◽

Author(s):

Anna Marie Pyle

Keyword(s):

Group Ii Intron ◽

Group Ii ◽

Splicing Systems

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

MATEMATIKA ◽

10.11113/matematika.v35.n4.1260 ◽

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.

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