Seed-Based Exclusion Method for Non-coding RNA Gene Search

Jean-Eudes Duchesne 1 Mathieu Giraud 2, 3 Nadia El-Mabrouk 1
1 DIRO - Département d'Informatique et de Recherche Opérationnelle [Montreal]
2 LIFL - Laboratoire d'Informatique Fondamentale de Lille
3 SEQUOIA - Sequential Learning
LIFL - Laboratoire d'Informatique Fondamentale de Lille, Inria Lille - Nord Europe
Abstract : Given an RNA family characterized by conserved sequences and folding constraints, the problem is to search for all the instances of the RNA family in a genomic database. As seed-based heuristics have been proved very efficient to accelerate the classical homology based search methods such as BLAST, we use a similar idea for RNA structures. We present an exclusion method for RNA search allowing for possible nucleotide insertion, deletion and substitution. It is based on a partition of the RNA stem-loops into consecutive seeds and a preprocessing of the target database. This algorithm can be used to improve time efficiency of current methods, and is guaranteed to find all occurrences that contain at least one exact seed.
Type de document :
Communication dans un congrès
13th Annual International Computing and Combinatorics Conference (COCOON 2007), Jul 2007, Banff, Canada. 4598, pp.27-39, 2007, LNCS. 〈10.1007/978-3-540-73545-8_6〉
Liste complète des métadonnées

Littérature citée [16 références]  Voir  Masquer  Télécharger
https://hal.inria.fr/inria-00271642
Contributeur : Mathieu Giraud <>
Soumis le : mercredi 9 avril 2008 - 17:55:55
Dernière modification le : jeudi 11 janvier 2018 - 06:22:13
Document(s) archivé(s) le : jeudi 20 mai 2010 - 23:11:51

Fichier

dgem-cocoon-07-lncs.pdf
Fichiers éditeurs autorisés sur une archive ouverte

Identifiants

Collections

INRIA | UNIV-LILLE3 | LIFL

Citation

Jean-Eudes Duchesne, Mathieu Giraud, Nadia El-Mabrouk. Seed-Based Exclusion Method for Non-coding RNA Gene Search. 13th Annual International Computing and Combinatorics Conference (COCOON 2007), Jul 2007, Banff, Canada. 4598, pp.27-39, 2007, LNCS. 〈10.1007/978-3-540-73545-8_6〉. 〈inria-00271642〉

Exporter

BibTeX TEI DC DCterms EndNote

Partager

Métriques

Consultations de la notice

526

Téléchargements de fichiers

154

Contact


archive-ouverte@inria.fr