Titre :

Efficient seeding techniques for protein similarity search

Auteur(s) :

Roytberg, Mihkail [Auteur]
Institute of Mathematical Problems in Biology [IMPB RAS]
Gambin, Anna [Auteur]
Institute of Informatics [Warsaw]
Noé, Laurent [Auteur correspondant]
Sequential Learning [SEQUOIA]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]
Lasota, Slawomir [Auteur]
Institute of Informatics [Warsaw]
Furletova, Eugenia [Auteur]
Institute of Mathematical Problems in Biology [IMPB RAS]
Szczurek, Ewa [Auteur]
Department Computational Molecular Biology [MPIMG Berlin]
Kucherov, Gregory [Auteur]
Sequential Learning [SEQUOIA]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]

Éditeur(s) ou directeur(s) scientifique(s) :

Elloumi
M and K\"{u}ng
J. and Linial
M. and Murphy
R.F. and Schneider
K. and Toma
C.

Titre de la manifestation scientifique :

Proceedings of the 2nd International Conference BIRD

Ville :

Vienna

Pays :

Autriche

Date de début de la manifestation scientifique :

2008-07

Titre de la revue :

Communications in Computer and Information Science

Éditeur :

Springer Berlin Heidelberg

Date de publication :

2008

Mot(s)-clé(s) en anglais :

spaced seeds
subset seeds
protein similarity search

Discipline(s) HAL :

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

Résumé en anglais : [en]

We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal sensitivity/selectivity ...
Lire la suite >We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal sensitivity/selectivity trade-offs. We propose several different design methods and use them to construct several alphabets.We then perform an analysis of seeds built over those alphabet and compare them with the standard Blastp seeding method [2,3], as well as with the family of vector seeds proposed in [4]. While the formalism of subset seed is less expressive (but less costly to implement) than the accumulative principle used in Blastp and vector seeds, our seeds show a similar or even better performance than Blastp on Bernoulli models of proteins compatible with the common BLOSUM62 matrix.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