Titre :

Subset seed extension to Protein BLAST

Auteur(s) :

Gambin, Anna [Auteur]
Faculty of Mathematics, Informatics, and Mechanics [Warsaw] [MIMUW]
Lasota, Slawomir [Auteur]
Faculty of Mathematics, Informatics, and Mechanics [Warsaw] [MIMUW]
Startek, Michal [Auteur]
Faculty of Mathematics, Informatics, and Mechanics [Warsaw] [MIMUW]
Sykulski, Maciej [Auteur]
Faculty of Mathematics, Informatics, and Mechanics [Warsaw] [MIMUW]
Noé, Laurent [Auteur]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]
Bioinformatics and Sequence Analysis [BONSAI]
Kucherov, Gregory [Auteur]
Laboratoire d'Informatique Gaspard-Monge [LIGM]

Titre de la manifestation scientifique :

Bioinformatics 2011 - International Conference on Bioinformatics Models, Methods and Algorithms

Ville :

Rome

Pays :

Italie

Date de début de la manifestation scientifique :

2011-01-26

Éditeur :

SciTePress

Date de publication :

2011

Mot(s)-clé(s) en anglais :

Sequence Analysis
Algorithms and Software Tools
Sequence alignment
Protein BLAST
Subset seed
DFA
Genetic algorithm

Discipline(s) HAL :

Sciences du Vivant [q-bio]/Bio-Informatique, Biologie Systémique [q-bio.QM]
Informatique [cs]/Bio-informatique [q-bio.QM]

Résumé en anglais : [en]

The seeding technique became central in the theory of sequence alignment and there are several efficient tools applying seeds to DNA homology search. Recently, a concept of subset seeds has been proposed for similarity ...
Lire la suite >The seeding technique became central in the theory of sequence alignment and there are several efficient tools applying seeds to DNA homology search. Recently, a concept of subset seeds has been proposed for similarity search in protein sequences. We experimentally evaluate the applicability of subset seeds to protein homology search. We advocate the use of multiple subset seeds derived from a hierarchical tree of amino acid residues. Our method computes, by an evolutionary algorithm, seeds that are specifically designed for a given protein family. The representation of seeds by deterministic finite automata (DFAs) is developed and built into the NCBI-BLAST software. This extended tool, named SeedBLAST, is compared to the original NCBI-BLAST and PSI-BLAST on several protein families. Our results demonstrate a superiority of SeedBLAST in terms of efficiency, especially in the case of twilight zone hits. SeedBLAST is an open source software freely available http://bioputer.mimuw.edu.pl/papers/sblast . Supplementary material and user manual are also provided.Lire moins >

Langue :

Anglais

Comité de lecture :

Oui

Audience :

Internationale

Vulgarisation :

Non

Projet ANR :

Comparison of Complete Genomes: an algorithmic and statistical approach to investigate the mechanisms of bacterial genome evolution

Collections :

• Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL) - UMR 9189

Source :

Harvested from HAL