title: H-BLAST: a fast protein sequence alignment toolkit on heterogeneous computers with GPUs.
abstract: The sequence alignment is a fundamental problem in bioinformatics. BLAST is a routinely used tool for this purpose with over 118 000 citations in the past two decades. As the size of bio-sequence databases grows exponentially, the computational speed of alignment softwares must be improved.
  
  
  
  We develop the heterogeneous BLAST (H-BLAST), a fast parallel search tool for a heterogeneous computer that couples CPUs and GPUs, to accelerate BLASTX and BLASTP-basic tools of NCBI-BLAST. H-BLAST employs a locally decoupled seed-extension algorithm for better performance on GPUs, and offers a performance tuning mechanism for better efficiency among various CPUs and GPUs combinations. H-BLAST produces identical alignment results as NCBI-BLAST and its computational speed is much faster than that of NCBI-BLAST. Speedups achieved by H-BLAST over sequential NCBI-BLASTP (resp. NCBI-BLASTX) range mostly from 4 to 10 (resp. 5 to 7.2). With 2 CPU threads and 2 GPUs, H-BLAST can be faster than 16-threaded NCBI-BLASTX. Furthermore, H-BLAST is 1.5-4 times faster than GPU-BLAST.
  
  
  
  https://github.com/Yeyke/H-BLAST.git.
  
  
  
  yux06@syr.edu.
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: School of Data and Computer Science, and Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, People's Republic of China.
authors.forename: Weicai
authors.initials: W
authors.lastname: Ye
authors.affiliation: School of Data and Computer Science, and Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, People's Republic of China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Chen
authors.affiliation: School of Data and Computer Science, and Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, People's Republic of China.
authors.forename: Yongdong
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: School of Data and Computer Science, and Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, People's Republic of China.|Professor Emeritus of Department of Mathematics, Syracuse University, Syracuse, NY 13244, USA.
authors.forename: Yuesheng
authors.initials: Y
authors.lastname: Xu
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D003196:Computer Graphics; D003201:Computers; D030561:Databases, Nucleic Acid; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D012984:Software; D013997:Time Factors
chemical_list: D011506:Proteins