Modelling Of Two Stages DNA Splicing Languages On De Bruijn Graph

Modelling Of Two Stages DNA Splicing Languages On De Bruijn Graph

Finding the sequence of the genome from its compositions as well as a mathematical graph is the most interesting topic in a field of DNA molecular. Since lack of technology is the big obstacle that biologists are facing to read a long sequence of the genome from beginning up to the end, therefore f...

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Main Authors: Mohammad Hassan, Mudaber, Yuhani, Yusof, Mohd Sham, Mohamad, Aizi Nor Mazila, Ramli, Wen, Li Lim
Format: Article
Language:English
English
Published: Penerbit Universiti Teknologi Malaysia 2016
Subjects:
Q Science (General)
Online Access:http://umpir.ump.edu.my/id/eprint/11804/
http://umpir.ump.edu.my/id/eprint/11804/
http://umpir.ump.edu.my/id/eprint/11804/
http://umpir.ump.edu.my/id/eprint/11804/1/Modelling%20Of%20Two%20Stages%20Dna%20Splicing%20Languages%20On%20De%20Bruijn%20Graph.pdf
http://umpir.ump.edu.my/id/eprint/11804/7/Modelling%20Of%20Two%20Stages%20DNA%20Splicing%20Languages%20On%20De%20Bruijn%20Graph.pdf
id ump-11804
recordtype eprints
spelling ump-118042018-07-26T02:07:00Z http://umpir.ump.edu.my/id/eprint/11804/ Modelling Of Two Stages DNA Splicing Languages On De Bruijn Graph Mohammad Hassan, Mudaber Yuhani, Yusof Mohd Sham, Mohamad Aizi Nor Mazila, Ramli Wen, Li Lim Q Science (General) Finding the sequence of the genome from its compositions as well as a mathematical graph is the most interesting topic in a field of DNA molecular. Since lack of technology is the big obstacle that biologists are facing to read a long sequence of the genome from beginning up to the end, therefore finding the compositions of the genome having very long sequence and also its description via de Bruijn graph is challenging or even impossible. In this paper, Yusof-Goode (Y-G) approach is used to generate the DNA splicing languages based on cutting sites of initial strings (one or two cutting sites) and crossing and contexts factors of restriction enzymes. The two short sequences of DNA (8bp) and two restriction enzymes are considered to create a connection between mathematics and DNA molecular. This relation will be presented as de Bruijn graph so that every edge of the de Bruijn graph gives a k-mer composition of DNA molecule and also each path of the de Bruijn graph gives a DNA sequence and vice-versa. Besides, the persistency and permanency of two stages DNA splicing languages can be predicted using this model. Penerbit Universiti Teknologi Malaysia 2016 Article PeerReviewed application/pdf en http://umpir.ump.edu.my/id/eprint/11804/1/Modelling%20Of%20Two%20Stages%20Dna%20Splicing%20Languages%20On%20De%20Bruijn%20Graph.pdf application/pdf en http://umpir.ump.edu.my/id/eprint/11804/7/Modelling%20Of%20Two%20Stages%20DNA%20Splicing%20Languages%20On%20De%20Bruijn%20Graph.pdf Mohammad Hassan, Mudaber and Yuhani, Yusof and Mohd Sham, Mohamad and Aizi Nor Mazila, Ramli and Wen, Li Lim (2016) Modelling Of Two Stages DNA Splicing Languages On De Bruijn Graph. Jurnal Teknologi (Sciences and Engineering), 78 (1). pp. 73-78. ISSN 0127-9696 (print); 2180-3722 (online) http://dx.doi.org/10.11113/jt.v78.4236 DOI: 10.11113/jt.v78.4236
repository_type Digital Repository
institution_category Local University
institution Universiti Malaysia Pahang
building UMP Institutional Repository
collection Online Access
language English
English
topic Q Science (General)
spellingShingle Q Science (General)
Mohammad Hassan, Mudaber
Yuhani, Yusof
Mohd Sham, Mohamad
Aizi Nor Mazila, Ramli
Wen, Li Lim
Modelling Of Two Stages DNA Splicing Languages On De Bruijn Graph
description Finding the sequence of the genome from its compositions as well as a mathematical graph is the most interesting topic in a field of DNA molecular. Since lack of technology is the big obstacle that biologists are facing to read a long sequence of the genome from beginning up to the end, therefore finding the compositions of the genome having very long sequence and also its description via de Bruijn graph is challenging or even impossible. In this paper, Yusof-Goode (Y-G) approach is used to generate the DNA splicing languages based on cutting sites of initial strings (one or two cutting sites) and crossing and contexts factors of restriction enzymes. The two short sequences of DNA (8bp) and two restriction enzymes are considered to create a connection between mathematics and DNA molecular. This relation will be presented as de Bruijn graph so that every edge of the de Bruijn graph gives a k-mer composition of DNA molecule and also each path of the de Bruijn graph gives a DNA sequence and vice-versa. Besides, the persistency and permanency of two stages DNA splicing languages can be predicted using this model.
format Article
author Mohammad Hassan, Mudaber
Yuhani, Yusof
Mohd Sham, Mohamad
Aizi Nor Mazila, Ramli
Wen, Li Lim
author_facet Mohammad Hassan, Mudaber
Yuhani, Yusof
Mohd Sham, Mohamad
Aizi Nor Mazila, Ramli
Wen, Li Lim
author_sort Mohammad Hassan, Mudaber
title Modelling Of Two Stages DNA Splicing Languages On De Bruijn Graph
title_short Modelling Of Two Stages DNA Splicing Languages On De Bruijn Graph
title_full Modelling Of Two Stages DNA Splicing Languages On De Bruijn Graph
title_fullStr Modelling Of Two Stages DNA Splicing Languages On De Bruijn Graph
title_full_unstemmed Modelling Of Two Stages DNA Splicing Languages On De Bruijn Graph
title_sort modelling of two stages dna splicing languages on de bruijn graph
publisher Penerbit Universiti Teknologi Malaysia
publishDate 2016
url http://umpir.ump.edu.my/id/eprint/11804/
http://umpir.ump.edu.my/id/eprint/11804/
http://umpir.ump.edu.my/id/eprint/11804/
http://umpir.ump.edu.my/id/eprint/11804/1/Modelling%20Of%20Two%20Stages%20Dna%20Splicing%20Languages%20On%20De%20Bruijn%20Graph.pdf
http://umpir.ump.edu.my/id/eprint/11804/7/Modelling%20Of%20Two%20Stages%20DNA%20Splicing%20Languages%20On%20De%20Bruijn%20Graph.pdf
first_indexed 2023-09-18T22:12:47Z
last_indexed 2023-09-18T22:12:47Z
_version_ 1777415138634104832

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