scholarly journals Descriptional Complexity of Semi-simple Splicing Systems

2020 ◽  
pp. 150-163
Author(s):  
Lila Kari ◽  
Timothy Ng
Keyword(s):  
Descriptional Complexity ◽  
Splicing Systems

ON SMALL UNIVERSAL SPLICING SYSTEMS

2012 ◽  
Vol 23 (07) ◽  
pp. 1423-1438 ◽  
Author(s):  
ARTIOM ALHAZOV ◽  
YURII ROGOZHIN ◽  
SERGEY VERLAN
Keyword(s):  
Test Tube ◽  
P System ◽  
Tube System ◽  
Descriptional Complexity ◽  
Splicing Systems

In this paper we consider universal systems based on splicing. As in previous works, we take the number of rules as the parameter for the descriptional complexity. We present three results: universal double splicing extended H system with 5 rules, universal splicing test tube system with 8 rules and a universal splicing P system with 5 rules.

scholarly journals Descriptional Complexity of Semi-Simple Splicing Systems

2021 ◽  
pp. 1-27
Author(s):  
Lila Kari ◽  
Timothy Ng
Keyword(s):  
Regular Language ◽  
Biological Process ◽  
Finite Automata ◽  
Dna Recombination ◽  
The Other ◽  
Binary String ◽  
Deterministic Finite Automata ◽  
Descriptional Complexity ◽  
Generative Mechanisms ◽  
Splicing Systems

Splicing systems are generative mechanisms introduced by Tom Head in 1987 to model the biological process of DNA recombination. The computational engine of a splicing system is the “splicing operation”, a cut-and-paste binary string operation defined by a set of “splicing rules”, quadruples [Formula: see text] where [Formula: see text] are words over an alphabet [Formula: see text]. For two strings [Formula: see text] and [Formula: see text], applying the splicing rule [Formula: see text] produces the string [Formula: see text]. In this paper we focus on a particular type of splicing systems, called [Formula: see text] semi-simple splicing systems, [Formula: see text] and [Formula: see text], wherein all splicing rules [Formula: see text] have the property that the two strings in positions [Formula: see text] and [Formula: see text] in [Formula: see text] are singleton letters, while the other two strings are empty. The language generated by such a system consists of the set of words that are obtained starting from an initial set called “axiom set”, by iteratively applying the splicing rules to strings in the axiom set as well as to intermediately produced strings. We consider semi-simple splicing systems where the axiom set is a regular language, and investigate the descriptional complexity of such systems in terms of the size of the minimal deterministic finite automata that recognize the languages they generate.

DESCRIPTIONAL COMPLEXITY OF SPLICING SYSTEMS

2008 ◽  
Vol 19 (04) ◽  
pp. 813-826 ◽  
Author(s):  
REMCO LOOS ◽  
ANDREAS MALCHER ◽  
DETLEF WOTSCHKE
Keyword(s):  
Lower Bounds ◽  
Finite Automata ◽  
Regular Languages ◽  
Upper And Lower Bounds ◽  
Descriptional Complexity ◽  
Nondeterministic Finite Automata ◽  
Total Length ◽  
Splicing Systems

In this paper, the descriptional complexity of extended finite splicing systems is studied. These systems are known to generate exactly the class of regular languages. Upper and lower bounds are shown relating the size of these splicing systems, defined as the total length of the rules and the initial language of the system, to the size of their equivalent minimal nondeterministic finite automata (NFA). In addition, an accepting model of extended finite splicing systems is studied. Using this variant one can obtain systems which are more than polynomially more succinct than the equivalent NFA or generating extended finite splicing system.

scholarly journals Accepting splicing systems

2010 ◽  
Vol 411 (25) ◽  
pp. 2414-2422 ◽  
Author(s):  
Victor Mitrana ◽  
Ion Petre ◽  
Vladimir Rogojin
Keyword(s):  
Splicing Systems

Algorithms for Splicing Systems

1992 ◽  
Vol 21 (3) ◽  
pp. 507-520 ◽  
Author(s):  
R. W. Gatterdam
Keyword(s):  
Splicing Systems

Multiset splicing systems

Biosystems ◽  
2004 ◽  
Vol 74 (1-3) ◽  
pp. 1-7 ◽  
Author(s):  
Jürgen Dassow ◽  
György Vaszil
Keyword(s):  
Splicing Systems

scholarly journals Computation of Splicing Languages from DNA Splicing System Based on Sequences of Restriction Enzymes

2019 ◽  
Vol 8 (6S3) ◽  
pp. 31-42
Keyword(s):  
Restriction Enzyme ◽  
Dna Computing ◽  
Restriction Enzymes ◽  
Visual Programming ◽  
Cleavage Pattern ◽  
Dna Molecules ◽  
Splicing Systems ◽  
Dna Splicing

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.

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

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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