Result: A SAT-based approach to multiple sequence alignment
Title:
A SAT-based approach to multiple sequence alignment
Authors:
Source:
CP 2003 : principles and practice of constraint programming (Kinsale, 29 September - 3 October 2003)Lecture notes in computer science. :940-944
Publisher Information:
Berlin: Springer, 2003.
Publication Year:
2003
Physical Description:
print, 11 ref
Original Material:
INIST-CNRS
Subject Terms:
Computer science, Informatique, Sciences exactes et technologie, Exact sciences and technology, Sciences appliquees, Applied sciences, Recherche operationnelle. Gestion, Operational research. Management science, Recherche opérationnelle et modèles formalisés de gestion, Operational research and scientific management, Programmation mathématique, Mathematical programming, Algorithme compétitif, Competitive algorithms, Algorithme recherche, Search algorithm, Algoritmo búsqueda, Alignement séquence, Sequence alignment, Alineación secuencia, Bioinformatique, Bioinformatics, Bioinformática, Coupe graphe, Graph cut, Corte grafo, Logique propositionnelle, Propositional logic, Lógica proposicional, Optimisation sous contrainte, Constrained optimization, Optimización con restricción, Programmation en nombres entiers, Integer programming, Programación entera, Programmation mathématique, Mathematical programming, Programación matemática, Satisfaction contrainte, Constraint satisfaction, Satisfaccion restricción, Théorie graphe, Graph theory, Teoría grafo, Graphe épars, Sparse graph, Recherche locale, Local search
Document Type:
Conference
Conference Paper
File Description:
text
Language:
English
Author Affiliations:
Cork Constraint Computation Centre, Cork, Ireland
Department of Biochemistry, University College, Cork, Ireland
Department of Biochemistry, University College, Cork, Ireland
ISSN:
0302-9743
Rights:
Copyright 2004 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
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:
Operational research. Management
Accession Number:
edscal.15716036
Database:
PASCAL Archive
Further Information
Multiple sequence alignment is a central problem in Bioinformatics. A known integer programming approach is to apply branch-and-cut to exponentially large graph-theoretic models. This paper describes a new integer program formulation that generates models small enough to be passed to generic solvers. The formulation is a hybrid relating the sparse alignment graph with a compact encoding of the alignment matrix via channelling constraints. Alignments obtained with a SAT-based local search algorithm are competitive with those of state-of-the-art algorithms, though execution times are much longer.