scholarly journals THE CHARACTERIZATIONS OF DIFFERENT SPLICING SYSTEMS

2012 ◽  
Vol 09 ◽  
pp. 89-94
Author(s):  
FARIBA KARIMI ◽  
NOR HANIZA SARMIN ◽  
FONG WAN HENG
Keyword(s):  
Formal Language ◽  
Biological Process ◽  
Dna Recombination ◽  
Restriction Enzymes ◽  
Theoretical Computer Science ◽  
Language Theory ◽  
Discrete Mathematics ◽  
Theoretical Computer ◽  
Points Of View ◽  
Splicing Systems

The concept of splicing system was first introduced by Head in 1987 to model the biological process of DNA recombination mathematically. This model was made on the basis of formal language theory which is a branch of applied discrete mathematics and theoretical computer science. In fact, splicing system treats DNA molecule and the recombinant behavior by restriction enzymes and ligases in the form of words and splicing rules respectively. The notion of splicing systems was taken into account from different points of view by many mathematicians. Several modified definitions have been introduced by many researchers. In this paper, some properties of different kinds of splicing systems are presented and their relationships are investigated. Furthermore, these results are illustrated by some examples.

scholarly journals Some relations on different types of splicing systems

2014 ◽  
Vol 6 (2) ◽  
Author(s):  
Yuhani Yusof ◽  
Nor Haniza Sarmin ◽  
Fong Wan Heng ◽  
Fariba Karimi
Keyword(s):  
Computer Science ◽  
Formal Language ◽  
Theoretical Computer Science ◽  
Language Theory ◽  
Discrete Mathematics ◽  
Generative Capacity ◽  
Theoretical Computer ◽  
Different Types ◽  
Splicing Systems

Splicing system is a formal characterization of the generative capacity of specified enzymatic activities acting on initial DNA molecules that was first initiated by Head in 1987. This splicing system is formally illustrated under the framework of Formal Language Theory which is a branch of Theoretical Computer Science and Applied Discrete Mathematics. There are many types of splicing systems including null-context, simple, semi-simple and seminull. In this paper, some relations for those types of splicing systems are presented.

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

MATEMATIKA ◽  
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.

scholarly journals Generalisations of DNA Splicing Systems with One Palindromic Restriction Enzyme

MATEMATIKA ◽  
2018 ◽  
Vol 34 (1) ◽  
pp. 59-71 ◽  
Author(s):  
Fong Wan Heng ◽  
Nurul Izzaty Ismail
Keyword(s):  
Restriction Enzyme ◽  
Formal Language ◽  
Restriction Enzymes ◽  
Potential Effect ◽  
Language Theory ◽  
Regular Expressions ◽  
Nitrogen Bases ◽  
Restriction Sites ◽  
Splicing Systems ◽  
Dna Splicing

In DNA splicing system, the potential effect of sets of restriction enzymes and a ligase that allow DNA molecules to be cleaved and re-associated to produce further molecules is modelled mathematically.  This modelling is done in the framework of formal language theory, in which the nitrogen bases, nucleotides and restriction sites are modelled as alphabets, strings and rules respectively.  The molecules resulting from a splicing system is depicted as the splicing language.  In this research, the splicing language resulting from DNA splicing systems with one palindromic restriction enzyme for one and two (non-overlapping) cutting sites are generalised as regular expressions.

scholarly journals Generalisations of Splicing Languages in DNA Splicing Systems Involving Two Palindromic Restriction Enzymes

2021 ◽  
Vol 17 (2) ◽  
pp. 128-138
Author(s):  
Wan Heng Fong ◽  
Nurul Izzaty Ismail ◽  
Nor Haniza Sarmin
Keyword(s):  
Restriction Enzyme ◽  
Dna Computing ◽  
Formal Language ◽  
Restriction Enzymes ◽  
Language Theory ◽  
Dna Molecules ◽  
Induction Method ◽  
Different Types ◽  
Splicing Systems ◽  
Dna Splicing

DNA splicing system is initiated by Head to mathematically model a relation between formal language theory and DNA molecules. In DNA splicing systems, DNA molecules are cut and recombined in specific ways with the existence of enzymes, which are also known as endonucleases, to produce further molecules. The resulting molecules are depicted as splicing languages by using concepts in formal languages theory. A sequence of restriction enzyme that reads the same forward and backward is called as a palindromic rule. Previously, researches on different types of splicing languages have been done. In this research, generalisations of splicing languages resulting from DNA splicing systems with non-overlapping cutting sites of two palindromic restriction enzymes are presented as theorems using the induction method. The results from this research are beneficial for researchers in the field of DNA computing since it contributes to the development of splicing languages generated from DNA splicing systems with different palindromic restriction enzymes by using these generalisations.

scholarly journals From the Quasi-Total Strong Differential to Quasi-Total Italian Domination in Graphs

Symmetry ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1036
Author(s):  
Abel Cabrera Martínez ◽  
Alejandro Estrada-Moreno ◽  
Juan Alberto Rodríguez-Velázquez
Keyword(s):  
Vertex Cover ◽  
Domination Number ◽  
Theoretical Computer Science ◽  
Discrete Mathematics ◽  
Special Issue ◽  
Total Domination Number ◽  
Theoretical Computer ◽  
Graph Parameters ◽  
Semitotal Domination ◽  
Domination In Graphs

This paper is devoted to the study of the quasi-total strong differential of a graph, and it is a contribution to the Special Issue “Theoretical computer science and discrete mathematics” of Symmetry. Given a vertex x∈V(G) of a graph G, the neighbourhood of x is denoted by N(x). The neighbourhood of a set X⊆V(G) is defined to be N(X)=⋃x∈XN(x), while the external neighbourhood of X is defined to be Ne(X)=N(X)∖X. Now, for every set X⊆V(G) and every vertex x∈X, the external private neighbourhood of x with respect to X is defined as the set Pe(x,X)={y∈V(G)∖X:N(y)∩X={x}}. Let Xw={x∈X:Pe(x,X)≠⌀}. The strong differential of X is defined to be ∂s(X)=|Ne(X)|−|Xw|, while the quasi-total strong differential of G is defined to be ∂s*(G)=max{∂s(X):X⊆V(G)andXw⊆N(X)}. We show that the quasi-total strong differential is closely related to several graph parameters, including the domination number, the total domination number, the 2-domination number, the vertex cover number, the semitotal domination number, the strong differential, and the quasi-total Italian domination number. As a consequence of the study, we show that the problem of finding the quasi-total strong differential of a graph is NP-hard.

scholarly journals Foreword to the special issue dedicated to the tenth ''Journées montoises d'informatique théorique''

2007 ◽  
Vol Vol. 9 no. 2 ◽  
Author(s):  
Véronique Bruyère ◽  
Michel Rigo
Keyword(s):  
Computer Science ◽  
Coding Theory ◽  
Theoretical Computer Science ◽  
Discrete Mathematics ◽  
Combinatorics On Words ◽  
Special Issue ◽  
Theoretical Computer ◽  
Universitair Centrum ◽  
Numeration Systems ◽  
The University

Held at the Institute of Mathematics of the University of Liège, Liège, September 8―11, 2004 International audience This special issue of Discrete Mathematics & Theoretical Computer Science is dedicated to the tenth "Journées montoises d'informatique théorique" conference (Mons theoretical computer science days) which was held, for the first time, at the Institute of Mathematics of the University of Liège, Belgium, From 8th to 11th September 2004. Previous editions of this conference took place in Mons 1990, 1992, 1994, 1998, in Rouen 1991, in Bordeaux 1993, Marseille 1995, Marne-La-Vallée 2000 and Montpellier 2002.<p> This tenth edition can be considered as a widely international one. We were lucky to have almost 85 participants from fourteen different countries: Austria, Belgium, Burkina Faso, Canada, Czech republic, Finland, France, Germany, Israel, Italy, Japan, Norway, Poland and Portugal. The main proportion of researchers participating to this event was coming from France and Italy where a long tradition of combinatorics on words is well established. During four days, 42 contributed talks and 7 invited talks were given, the main topics being combinatorics on words, numeration systems, automata and formal languages theory, coding theory, verification, bio-informatics, number theory, grammars, text algorithms, symbolic dynamics and tilings. The invited speakers were: J. Cassaigne (CNRS, Luminy-Marseille), D. Caucal (IRISIA-CNRS, Rennes), C. Frougny (LIAFA, Université Paris 8), T. Helleseth (University of Bergen), S. Langerman (FNRS, Université Libre de Bruxelles), F. Neven (Limburgs Universitair Centrum, Diepenbeek), M.-F. Sagot (Inria Rhône-Alpes, Université Lyon I).<p> We would like to thanks all the participants, the invited speakers and the anonymous referees who made possible this event and special issue. Each paper has been refereed using high scientific standard by two independent referees. Readers of this special issue may wonder why it took so long to obtain it. We have encountered some problems with the formerly chosen journal and for the benefit of the contributors to this issue, we have chosen Discrete Mathematics & Theoretical Computer Science to publish their work.

scholarly journals Open k-monopolies in graphs: complexity and related concepts

2016 ◽  
Vol Vol. 18 no. 3 (Graph Theory) ◽  
Author(s):  
Dorota Kuziak ◽  
Iztok Peterin ◽  
Ismael G. Yero
Keyword(s):  
Positive Integer ◽  
Computer Science ◽  
Long Range ◽  
Theoretical Computer Science ◽  
Chordal Graphs ◽  
Discrete Mathematics ◽  
Voting Systems ◽  
Minimum Cardinality ◽  
Theoretical Computer ◽  
Np Complete

Closed monopolies in graphs have a quite long range of applications in several problems related to overcoming failures, since they frequently have some common approaches around the notion of majorities, for instance to consensus problems, diagnosis problems or voting systems. We introduce here open $k$-monopolies in graphs which are closely related to different parameters in graphs. Given a graph $G=(V,E)$ and $X\subseteq V$, if $\delta_X(v)$ is the number of neighbors $v$ has in $X$, $k$ is an integer and $t$ is a positive integer, then we establish in this article a connection between the following three concepts: - Given a nonempty set $M\subseteq V$ a vertex $v$ of $G$ is said to be $k$-controlled by $M$ if $\delta_M(v)\ge \frac{\delta_V(v)}{2}+k$. The set $M$ is called an open $k$-monopoly for $G$ if it $k$-controls every vertex $v$ of $G$. - A function $f: V\rightarrow \{-1,1\}$ is called a signed total $t$-dominating function for $G$ if $f(N(v))=\sum_{v\in N(v)}f(v)\geq t$ for all $v\in V$. - A nonempty set $S\subseteq V$ is a global (defensive and offensive) $k$-alliance in $G$ if $\delta_S(v)\ge \delta_{V-S}(v)+k$ holds for every $v\in V$. In this article we prove that the problem of computing the minimum cardinality of an open $0$-monopoly in a graph is NP-complete even restricted to bipartite or chordal graphs. In addition we present some general bounds for the minimum cardinality of open $k$-monopolies and we derive some exact values. Comment: 18 pages, Discrete Mathematics & Theoretical Computer Science (2016)

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