The representation of n-cutting site splicing languages for a single string with palindromic rule via de Bruijn graph

Yusof-Goode (Y-G) splicing system proposed by Yusof illustrates the deoxyribonucleic acid (DNA) splicing process in a luminous way, where the rule is written in a double triple notation. In the process of generating splicing languages, DNA molecules are cut and pasted, based on the reaction of the...

Full description

Saved in:
Bibliographic Details
Main Authors: Mohd Ruslim, Nooradelena, Yuhani, Yusof, Mohd Sham, Mohamad
Format: Conference or Workshop Item
Language:English
Published: AIP Publishing 2024
Subjects:
Online Access:http://umpir.ump.edu.my/id/eprint/41401/1/240307_Adelena.pdf
http://umpir.ump.edu.my/id/eprint/41401/
https://doi.org/10.1063/5.0192296
https://doi.org/10.1063/5.0192296
Tags: Add Tag
No Tags, Be the first to tag this record!
Institution: Universiti Malaysia Pahang Al-Sultan Abdullah
Language: English
id my.ump.umpir.41401
record_format eprints
spelling my.ump.umpir.414012024-12-31T04:00:57Z http://umpir.ump.edu.my/id/eprint/41401/ The representation of n-cutting site splicing languages for a single string with palindromic rule via de Bruijn graph Mohd Ruslim, Nooradelena Yuhani, Yusof Mohd Sham, Mohamad QA Mathematics Yusof-Goode (Y-G) splicing system proposed by Yusof illustrates the deoxyribonucleic acid (DNA) splicing process in a luminous way, where the rule is written in a double triple notation. In the process of generating splicing languages, DNA molecules are cut and pasted, based on the reaction of the molecules with restriction enzyme and ligase. The resulting molecules, either in original or new molecules can be classified mathematically in the form of limit, adult or transient languages. Conducting a wet lab experiment to produce splicing languages is a huge investment, thus mathematical approach is one of the best options in predicting the outcome on splicing languages when n-cutting site exist in a splicing process. Besides the generation of splicing languages through splicing system, a meaningful representation of the languages can be portrayed in a graph. In this paper, the n-cutting site splicing languages generated from Y-G splicing system containing single string with 2-cutting site, with palindromic rule and palindromic crossing site is investigated. The features of left and right contexts of the rule are considered in the two cases discussed in this paper. Besides, two new definitions namely connectors and sub-connectors are given and are adopted in the generation of de Bruijn graph. With the constructed de Bruijn graph for the resulting splicing languages from both cases, a theorem is proposed. AIP Publishing 2024-03-07 Conference or Workshop Item PeerReviewed pdf en http://umpir.ump.edu.my/id/eprint/41401/1/240307_Adelena.pdf Mohd Ruslim, Nooradelena and Yuhani, Yusof and Mohd Sham, Mohamad (2024) The representation of n-cutting site splicing languages for a single string with palindromic rule via de Bruijn graph. In: AIP Conference Proceedings. AIP Conference Proceedings; 3rd International Conference on Applied and Industrial Mathematics and Statistics 2022, ICoAIMS 2022 , 24 - 26 August 2022 , Virtual, Online. pp. 1-10., 2895 (1). ISSN 0094-243X (Published) https://doi.org/10.1063/5.0192296 https://doi.org/10.1063/5.0192296
institution Universiti Malaysia Pahang Al-Sultan Abdullah
building UMPSA Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Malaysia Pahang Al-Sultan Abdullah
content_source UMPSA Institutional Repository
url_provider http://umpir.ump.edu.my/
language English
topic QA Mathematics
spellingShingle QA Mathematics
Mohd Ruslim, Nooradelena
Yuhani, Yusof
Mohd Sham, Mohamad
The representation of n-cutting site splicing languages for a single string with palindromic rule via de Bruijn graph
description Yusof-Goode (Y-G) splicing system proposed by Yusof illustrates the deoxyribonucleic acid (DNA) splicing process in a luminous way, where the rule is written in a double triple notation. In the process of generating splicing languages, DNA molecules are cut and pasted, based on the reaction of the molecules with restriction enzyme and ligase. The resulting molecules, either in original or new molecules can be classified mathematically in the form of limit, adult or transient languages. Conducting a wet lab experiment to produce splicing languages is a huge investment, thus mathematical approach is one of the best options in predicting the outcome on splicing languages when n-cutting site exist in a splicing process. Besides the generation of splicing languages through splicing system, a meaningful representation of the languages can be portrayed in a graph. In this paper, the n-cutting site splicing languages generated from Y-G splicing system containing single string with 2-cutting site, with palindromic rule and palindromic crossing site is investigated. The features of left and right contexts of the rule are considered in the two cases discussed in this paper. Besides, two new definitions namely connectors and sub-connectors are given and are adopted in the generation of de Bruijn graph. With the constructed de Bruijn graph for the resulting splicing languages from both cases, a theorem is proposed.
format Conference or Workshop Item
author Mohd Ruslim, Nooradelena
Yuhani, Yusof
Mohd Sham, Mohamad
author_facet Mohd Ruslim, Nooradelena
Yuhani, Yusof
Mohd Sham, Mohamad
author_sort Mohd Ruslim, Nooradelena
title The representation of n-cutting site splicing languages for a single string with palindromic rule via de Bruijn graph
title_short The representation of n-cutting site splicing languages for a single string with palindromic rule via de Bruijn graph
title_full The representation of n-cutting site splicing languages for a single string with palindromic rule via de Bruijn graph
title_fullStr The representation of n-cutting site splicing languages for a single string with palindromic rule via de Bruijn graph
title_full_unstemmed The representation of n-cutting site splicing languages for a single string with palindromic rule via de Bruijn graph
title_sort representation of n-cutting site splicing languages for a single string with palindromic rule via de bruijn graph
publisher AIP Publishing
publishDate 2024
url http://umpir.ump.edu.my/id/eprint/41401/1/240307_Adelena.pdf
http://umpir.ump.edu.my/id/eprint/41401/
https://doi.org/10.1063/5.0192296
https://doi.org/10.1063/5.0192296
_version_ 1822924871152173056