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...
| Main Authors: | , , |
|---|---|
| Format: | Conference or Workshop Item |
| Language: | English |
| Published: |
AIP Publishing
2024
|
| Subjects: | |
| Online Access: | http://umpir.ump.edu.my/id/eprint/41401/ http://umpir.ump.edu.my/id/eprint/41401/1/240307_Adelena.pdf |
| _version_ | 1848826325408677888 |
|---|---|
| author | Mohd Ruslim, Nooradelena Yuhani, Yusof Mohd Sham, Mohamad |
| author_facet | Mohd Ruslim, Nooradelena Yuhani, Yusof Mohd Sham, Mohamad |
| author_sort | Mohd Ruslim, Nooradelena |
| building | UMP Institutional Repository |
| collection | Online Access |
| 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. |
| first_indexed | 2025-11-15T03:43:01Z |
| format | Conference or Workshop Item |
| id | ump-41401 |
| institution | Universiti Malaysia Pahang |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T03:43:01Z |
| publishDate | 2024 |
| publisher | AIP Publishing |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | ump-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 |
| 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 |
| title | 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_short | 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 |
| topic | QA Mathematics |
| url | http://umpir.ump.edu.my/id/eprint/41401/ http://umpir.ump.edu.my/id/eprint/41401/ http://umpir.ump.edu.my/id/eprint/41401/ http://umpir.ump.edu.my/id/eprint/41401/1/240307_Adelena.pdf |