Title :

Efficient seeding techniques for protein similarity search

Author(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]

Scientific editor(s) :

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

Conference title :

Proceedings of the 2nd International Conference BIRD

City :

Vienna

Country :

Autriche

Start date of the conference :

2008-07

Journal title :

Communications in Computer and Information Science

Publisher :

Springer Berlin Heidelberg

Publication date :

2008

English keyword(s) :

spaced seeds
subset seeds
protein similarity search

HAL domain(s) :

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

English abstract : [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 ...
Show more >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.Show less >

Language :

Anglais

Peer reviewed article :

Oui

Audience :

Internationale

Popular science :

Non

ANR Project :

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