Title :

A Scalable Indexing Solution to Mine Huge Genomic Sequence Collections

Author(s) :

Rivals, Eric [Auteur correspondant]
Méthodes et Algorithmes pour la Bioinformatique [MAB]
Philippe, Nicolas [Auteur]
Méthodes et Algorithmes pour la Bioinformatique [MAB]
Salson, Mikael [Auteur]
Bioinformatics and Sequence Analysis [BONSAI]
Léonard, Martine [Auteur]
Laboratoire d'Informatique, de Traitement de l'Information et des Systèmes [LITIS]
Commes, Thérèse [Auteur]
Centre de recherche en Biologie Cellulaire [CRBM]
Lecroq, Thierry [Auteur]
Laboratoire d'Informatique, de Traitement de l'Information et des Systèmes [LITIS]

Journal title :

ERCIM News

Pages :

20-21

Publisher :

ERCIM

Publication date :

2012-04-02

ISSN :

0926-4981

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]

With High Throughput Sequencing (HTS) technologies, biology is experiencing a sequence data deluge. A single sequencing experiment currently yields 100 million short sequences, or reads, the analysis of which demands ...
Show more >With High Throughput Sequencing (HTS) technologies, biology is experiencing a sequence data deluge. A single sequencing experiment currently yields 100 million short sequences, or reads, the analysis of which demands efficient and scalable sequence analysis algorithms. Diverse kinds of applications repeatedly need to query the sequence collection for the occurrence positions of a subword. Time can be saved by building an index of all subwords present in the sequences before performing huge numbers of queries. However, both the scalability and the memory requirement of the chosen data structure must suit the data volume. Here, we introduce a novel indexing data structure, called Gk arrays, and related algorithms that improve on classical indexes and state of the art hash tables.Show less >

Language :

Anglais

Peer reviewed article :

Oui

Audience :

Internationale

Popular science :

Non

Collections :

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

Source :

Harvested from HAL