PLAST: parallel local alignment search tool for database comparison (2009)
Nguyen, Van Hoa, Lavenier, Dominique
Abstract Background Sequence similarity searching is an important and challenging task in molecular biology and next-generation sequencing should further strengthen the need for faster algorithms to...
Implementing Protein Seed-Based Comparison Algorithm on the SGI RASC-100 Platform (2009)
Nguyen, Van Hoa, Cornu, Alexandre, Lavenier, Dominique
This paper describes a parallel FPGA implementation of a genomic sequence comparison algorithm for finding similarities between a large set of protein sequences and full genomes. Results comparable...
Implementing Protein Seed-Based Comparison Algorithm on the SGI RASC-100 Platform (2009)
Nguyen, Van Hoa, Cornu, Alexandre, Lavenier, Dominique
This paper describes a parallel FPGA implementation of a genomic sequence comparison algorithm for finding similarities between a large set of protein sequences and full genomes. Results comparable...
PLAST: parallel local alignment search tool for database comparison (2009)
Nguyen, Van Hoa, Lavenier, Dominique
Sequence similarity searching is an important and challenging task in molecular biology and next-generation sequencing should further strengthen the need for faster algorithms to process such vast...
PLAST: parallel local alignment search tool for database comparison (2009)
Nguyen, Van Hoa, Lavenier, Dominique
Sequence similarity searching is an important and challenging task in molecular biology and next-generation sequencing should further strengthen the need for faster algorithms to process such vast...
Traitement parallèle des comparaisons intensives de séquences génomiques (2009)
La comparaison de séquences est une des tâches fondamentales de la bioinformatique. Les nouvelles technologies de séquençage conduisent à une production accélérée des données génomiques et...
Traitement parallèle des comparaisons intensives de séquences génomiques (2009)
La comparaison de séquences est une des tâches fondamentales de la bioinformatique. Les nouvelles technologies de séquençage conduisent à une production accélérée des données génomiques et...
Traitement parallèle des comparaisons intensives de séquences génomiques (2009)
La comparaison de séquences est une des tâches fondamentales de la bioinformatique. Les nouvelles technologies de séquençage conduisent à une production accélérée des données génomiques et...
Fine-grained parallelization of similarity search between protein sequences (2008)
Nguyen, Van Hoa, Lavenier, Dominique
This report presents the implementation of a protein sequence comparison algorithm specifically designed for speeding up time consuming part on parallel hardware such as SSE instructions, multicore...
Fine-grained parallelization of similarity search between protein sequences (2008)
Nguyen, Van Hoa, Lavenier, Dominique
This report presents the implementation of a protein sequence comparison algorithm specifically designed for speeding up time consuming part on parallel hardware such as SSE instructions, multicore...
Fine-grained parallelization of similarity search between protein sequences (2008)
Nguyen, Van Hoa, Lavenier, Dominique
This report presents the implementation of a protein sequence comparison algorithm specifically designed for speeding up time consuming part on parallel hardware such as SSE instructions, multicore...
Fine-grained parallelization of similarity search between protein sequences (2008)
Nguyen, Van Hoa, Lavenier, Dominique
This report presents the implementation of a protein sequence comparison algorithm specifically designed for speeding up time consuming part on parallel hardware such as SSE instructions, multicore...
Speeding up Subset Seed Algorithm for Intensive Protein Sequence Comparison (2008)
Nguyen, Van Hoa, Lavenier, Dominique
Sequence similarity search is a common and repeated task in molecular biology. The rapid growth of genomic databases leads to the need of speeding up the treatment of this task. In this paper, we...
Parallélisation de la recherche de similarités entre séquences protéiques sur GPU (2008)
Nguyen, Van Hoa, Lavenier, Dominique
Ce papier présente une nouvelle approche pour accélérer la recherche de similarités entre séquences protéiques. Elle repose sur une indexation complète des données en mémoire permettant...
Speeding up Subset Seed Algorithm for Intensive Protein Sequence Comparison (2008)
Nguyen, Van Hoa, Lavenier, Dominique
Sequence similarity search is a common and repeated task in molecular biology. The rapid growth of genomic databases leads to the need of speeding up the treatment of this task. In this paper, we...
Parallélisation de la recherche de similarités entre séquences protéiques sur GPU (2008)
Nguyen, Van Hoa, Lavenier, Dominique
Ce papier présente une nouvelle approche pour accélérer la recherche de similarités entre séquences protéiques. Elle repose sur une indexation complète des données en mémoire permettant...
Efficient Parallelization of a Protein Sequence Comparison Algorithm on Manycore Architecture (2008)
Ye, Xioachun, Nguyen, Van Hoa, Lavenier, Dominique, Fan, Dongrui
This paper introduces the Godson-T manycore architecture and demonstrates the efficiency of its synchronization mechanism through a computation intensive bioinformatics application: the comparison of...
Efficient Parallelization of a Protein Sequence Comparison Algorithm on Manycore Architecture (2008)
Ye, Xioachun, Nguyen, Van Hoa, Lavenier, Dominique, Fan, Dongrui
This paper introduces the Godson-T manycore architecture and demonstrates the efficiency of its synchronization mechanism through a computation intensive bioinformatics application: the comparison of...
Nguyen, Van Hoa, Lavenier, Dominique
This paper presents a method for speeding up the comparison of two protein banks. It is based on two techniques: bank indexing and fast computation of short alignments using the SIMD instruction set...
Nguyen, Van Hoa, Lavenier, Dominique
This paper presents a method for speeding up the comparison of two protein banks. It is based on two techniques: bank indexing and fast computation of short alignments using the SIMD instruction set...
Optimal neighborhood indexing for protein similarity search (2008)
Peterlongo, Pierre, Noé, Laurent, Lavenier, Dominique, Nguyen, Van Hoa, Kucherov, Gregory, Giraud, Mathieu
Similarity inference, one of the main bioinformatics tasks, has to face an exponential growth of the biological data. A classical approach used to cope with this data flow involves heuristics with...
Optimal neighborhood indexing for protein similarity search (2008)
Peterlongo, Pierre, Noé, Laurent, Lavenier, Dominique, Nguyen, Van Hoa, Kucherov, Gregory, Giraud, Mathieu
Similarity inference, one of the main bioinformatics tasks, has to face an exponential growth of the biological data. A classical approach used to cope with this data flow involves heuristics with...
Optimal neighborhood indexing for protein similarity search (2008)
Pierre Peterlongo, Laurent Noé, Dominique Lavenier, Van Hoa Nguyen, Gregory Kucherov, Mathieu Giraud
Background Similarity inference, one of the main bioinformatics tasks, has to face an exponential growth of the biological data. A classical approach used to cope with this data flow involves...
Recherche dans les banques d'ADN par indexation parallèle (2006)
Nguyen, Van Hoa, Lavenier, Dominique
Une des tâches de base de la biologie moléculaire est la recherche de similarités dans les banques d'ADN. Une recherche rapide passe par une mise en oeuvre parallèle des algorithmes. Les...
Recherche dans les banques d'ADN par indexation parallèle (2006)
Nguyen, Van Hoa, Lavenier, Dominique
Une des tâches de base de la biologie moléculaire est la recherche de similarités dans les banques d'ADN. Une recherche rapide passe par une mise en oeuvre parallèle des algorithmes. Les...