Treffer: Novel tree edit operations for RNA secondary structure comparison

Title:
Novel tree edit operations for RNA secondary structure comparison
Authors:
ALLALI, Julien, SAGOT, Marie-France
Source:
Algorithms in bioinformatics (Bergen, 17-21 September 2004)Lecture notes in computer science. :412-425
Publisher Information:
Berlin: Springer, 2004.
Publication Year:
2004
Physical Description:
print, 9 ref
Original Material:
INIST-CNRS
Subject Terms:
Genetics, Génétique, 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, Algorithmique. Calculabilité. Arithmétique ordinateur, Algorithmics. Computability. Computer arithmetics, Sciences biologiques et medicales, Biological and medical sciences, Sciences biologiques fondamentales et appliquees. Psychologie, Fundamental and applied biological sciences. Psychology, Generalites, General aspects, Mathématiques biologiques. Statistiques. Modèles. Métrologie. Informatique en biologie (généralités), Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects), Bioinformatique, Bioinformatics, Bioinformática, Complexité algorithme, Algorithm complexity, Complejidad algoritmo, RNA, Structure secondaire, Secondary structure, Estructura secundaria
Document Type:
Konferenz Conference Paper
File Description:
text
Language:
English
Author Affiliations:
Institut Gaspard-Monge, Université de Marne-la-Vallée, Cité Descartes, Champs-sur-Marne, 77454 Marne-la-Vallée, France
Inria Rhône-Alpes, Université Claude Bernard, Lyon I, 43 Bd du 11 Novembre 1918, 69622 Villeurbanne, France
King's College, London, United Kingdom
ISSN:
0302-9743
Access URL:
http://pascal-francis.inist.fr/vibad/index.php?action=search&terms=16144161
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
Notes:
Biological sciences. Generalities. Modelling. Methods

Computer science; theoretical automation; systems

Generalities in biological sciences
Accession Number:
edscal.16144161
Database:
PASCAL Archive

Weitere Informationen

We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two novel operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion and relabelling classically used in the literature. This allows us to address some serious limitations of the more traditional tree edit operations when the trees represent RNAs and what is searched for is a common structural core of two RNAs. Although the algorithm complexity has an exponential term, this term depends only on the number of successive fusions that may be applied to a same node, not on the total number of fusions. The algorithm remains therefore efficient in practice and is used for illustrative purposes on ribosomal as well as on other types of RNAs.