Seed design framework for mapping SOLiD reads
Type de document :
Communication dans un congrès avec actes
Titre :
Seed design framework for mapping SOLiD reads
Auteur(s) :
Noé, Laurent [Auteur correspondant]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]
Algorithms for large scale sequence analysis [SEQUOIA2]
Gîrdea, Marta [Auteur]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]
Algorithms for large scale sequence analysis [SEQUOIA2]
Kucherov, Gregory [Auteur]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]
Sequential Learning [SEQUOIA]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]
Algorithms for large scale sequence analysis [SEQUOIA2]
Gîrdea, Marta [Auteur]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]
Algorithms for large scale sequence analysis [SEQUOIA2]
Kucherov, Gregory [Auteur]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]
Sequential Learning [SEQUOIA]
Titre de la manifestation scientifique :
RECOMB
Ville :
Lisbon
Pays :
Portugal
Date de début de la manifestation scientifique :
2010-08-12
Titre de l’ouvrage :
Proc. RECOMB 2010
Titre de la revue :
Lecture Notes in Computer Science
Éditeur :
Springer
Date de publication :
2010
Mot(s)-clé(s) en anglais :
read mapping
spaced seeds design
Applied Biosystems SOLiD
spaced seeds design
Applied Biosystems SOLiD
Discipline(s) HAL :
Sciences du Vivant [q-bio]/Bio-Informatique, Biologie Systémique [q-bio.QM]
Informatique [cs]/Bio-informatique [q-bio.QM]
Informatique [cs]/Bio-informatique [q-bio.QM]
Résumé en anglais : [en]
The advent of high-throughput sequencing technologies con- stituted a major advance in genomic studies, offering new prospects in a wide range of applications. We propose a rigorous and flexible algorithmic solution to ...
Lire la suite >The advent of high-throughput sequencing technologies con- stituted 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 faith- ful 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.Lire moins >
Lire la suite >The advent of high-throughput sequencing technologies con- stituted 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 faith- ful 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.Lire moins >
Langue :
Anglais
Comité de lecture :
Oui
Audience :
Internationale
Vulgarisation :
Non
Collections :
Source :
Fichiers
- https://hal.inria.fr/inria-00484642/document
- Accès libre
- Accéder au document
- http://arxiv.org/pdf/1006.2625
- Accès libre
- Accéder au document
- https://hal.inria.fr/inria-00484642/document
- Accès libre
- Accéder au document
- document
- Accès libre
- Accéder au document
- maps.pdf
- Accès libre
- Accéder au document
- 1006.2625
- Accès libre
- Accéder au document