Title :

Designing Efficient Spaced Seeds for SOLiD Read Mapping.

Author(s) :

Noé, Laurent [Auteur]
Sequential Learning [SEQUOIA]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]
Gîrdea, Marta [Auteur]
Sequential Learning [SEQUOIA]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]
Kucherov, Gregory [Auteur]
Sequential Learning [SEQUOIA]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]

Journal title :

Advances in Bioinformatics

Publisher :

Hindawi Publishing Corporation

Publication date :

2010

ISSN :

1687-8027

English keyword(s) :

Spaced seeds
seed design
read mapping
Applied Biosystems SOLiD
color space alignment

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]

The advent of high-throughput sequencing technologies constituted a major advance in genomic studies, offering new prospects in a wide range of applications.We propose a rigorous and flexible algorithmic solution to mapping ...
Show more >The advent of high-throughput sequencing technologies constituted a major advance in genomic studies, offering new prospects in a wide range of applications.We propose a rigorous and flexible algorithmic solution to mapping SOLiD color-space reads to a reference genome. The solution relies on an advanced method of seed design that uses a faithful probabilistic model of read matches and, on the other hand, a novel seeding principle especially adapted to read mapping. Our method can handle both lossy and lossless frameworks and is able to distinguish, at the level of seed design, between SNPs and reading errors. We illustrate our approach by several seed designs and demonstrate their efficiency.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