Speeding up Subset Seed Algorithm for Intensive Protein Sequence Comparison - Archive ouverte HAL Access content directly
Conference Papers Year : 2008

Speeding up Subset Seed Algorithm for Intensive Protein Sequence Comparison

(1) , (1)
1

Abstract

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 present a subset seed algorithm for intensive protein sequence comparison. We have accelerated this algorithm by using indexing technique and fine grained parallelism of GPU and SIMD instructions. We have implemented two programs: iBLASTP, iTBLASTN. The GPU (SIMD) implementation of the two programs achieves a speed up ranging from 5.5 to 10 (4 to 5.6) compared to the BLASTP and TBLASTN of the BLAST program family, with comparable sensitivity.
Fichier principal
Vignette du fichier
rivf08.pdf (335.12 Ko) Télécharger le fichier
Origin : Files produced by the author(s)
Loading...

Dates and versions

inria-00321457 , version 1 (15-09-2008)

Identifiers

  • HAL Id : inria-00321457 , version 1

Cite

van Hoa Nguyen, Dominique Lavenier. Speeding up Subset Seed Algorithm for Intensive Protein Sequence Comparison. 6th IEEE International Conference on research, innovation & vision for the future, Jul 2008, Ho Chi Minh Ville, Vietnam. ⟨inria-00321457⟩
412 View
193 Download

Share

Gmail Facebook Twitter LinkedIn More