Treffer: Randomized fast design of short DNA words

Title:
Randomized fast design of short DNA words
Authors:
KAO, Ming-Yang, SANGHI, Manan, SCHWELLER, Robert
Source:
Automata, languages and programming (Lisbon, 11-15 July 2005)Lecture notes in computer science. :1275-1286
Publisher Information:
Berlin: Springer, 2005.
Publication Year:
2005
Physical Description:
print, 17 ref
Original Material:
INIST-CNRS
Subject Terms:
Computer science, Informatique, Sciences exactes et technologie, Exact sciences and technology, Sciences appliquees, Applied sciences, Informatique; automatique theorique; systemes, Computer science; control theory; systems, Informatique théorique, Theoretical computing, Automates. Machines abstraites. Machines de turing, Automata. Abstract machines. Turing machines, Algorithme génétique, Genetic algorithm, Algoritmo genético, Algorithme recherche, Search algorithm, Algoritmo búsqueda, Approche probabiliste, Probabilistic approach, Enfoque probabilista, Autoassemblage, Self assembly, Autoensamble, Automate, Automaton, Autómata, Chaîne caractère, Character string, Cadena carácter, DNA, Longueur mot, Word length, Longitud palabra, Méthode heuristique, Heuristic method, Método heurístico, Optimisation, Optimization, Optimización, Plan randomisé, Randomized design, Plan aleatorizado, Problème combinatoire, Combinatorial problem, Problema combinatorio, Programmation mathématique, Mathematical programming, Programación matemática, Recherche locale, Local search, Busca local, Temps polynomial, Polynomial time, Tiempo polinomial
Document Type:
Konferenz Conference Paper
File Description:
text
Language:
English
Author Affiliations:
Department of Computer Science, Northwestern University, Evanston, IL 60201, United States
ISSN:
0302-9743
Access URL:
http://pascal-francis.inist.fr/vibad/index.php?action=search&terms=16991570
Rights:
Copyright 2005 INIST-CNRS
CC BY 4.0
Sauf mention contraire ci-dessus, le contenu de cette notice bibliographique peut être utilisé dans le cadre d’une licence CC BY 4.0 Inist-CNRS / Unless otherwise stated above, the content of this bibliographic record may be used under a CC BY 4.0 licence by Inist-CNRS / A menos que se haya señalado antes, el contenido de este registro bibliográfico puede ser utilizado al amparo de una licencia CC BY 4.0 Inist-CNRS
Notes:
Computer science; theoretical automation; systems
Accession Number:
edscal.16991570
Database:
PASCAL Archive

Weitere Informationen

We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous work has extended results from coding theory to obtain bounds on code size for new biologically motivated constraints and has applied heuristic local search and genetic algorithm techniques for code design. This paper proposes a natural optimization formulation of the DNA code design problem in which the goal is to design n strings that satisfy a given set of constraints while minimizing the length of the strings. For multiple sets of constraints, we provide high-probability algorithms that run in time polynomial in n and any given constraint parameters, and output strings of length within a constant factor of the optimal. To the best of our knowledge, this work is the first to consider this type of optimization problem in the context of DNA code design.