title: GPU-Acceleration of Sequence Homology Searches with Database Subsequence Clustering.
abstract: Sequence homology searches are used in various fields and require large amounts of computation time, especially for metagenomic analysis, owing to the large number of queries and the database size. To accelerate computing analyses, graphics processing units (GPUs) are widely used as a low-cost, high-performance computing platform. Therefore, we mapped the time-consuming steps involved in GHOSTZ, which is a state-of-the-art homology search algorithm for protein sequences, onto a GPU and implemented it as GHOSTZ-GPU. In addition, we optimized memory access for GPU calculations and for communication between the CPU and GPU. As per results of the evaluation test involving metagenomic data, GHOSTZ-GPU with 12 CPU threads and 1 GPU was approximately 3.0- to 4.1-fold faster than GHOSTZ with 12 CPU threads. Moreover, GHOSTZ-GPU with 12 CPU threads and 3 GPUs was approximately 5.8- to 7.7-fold faster than GHOSTZ with 12 CPU threads.
authors.affiliation: Graduate School of Information Science and Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.|Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.
authors.forename: Shuji
authors.initials: S
authors.lastname: Suzuki
authors.affiliation: Graduate School of Information Science and Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.
authors.forename: Masanori
authors.initials: M
authors.lastname: Kakuta
authors.affiliation: Graduate School of Information Science and Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.|Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Ishida
authors.affiliation: Graduate School of Information Science and Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.|Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Akiyama
mesh_terms: D000465:Algorithms; D000818:Animals; D016000:Cluster Analysis; D003196:Computer Graphics; D003205:Computing Methodologies; D004247:DNA / Q000737:chemistry; D030541:Databases, Genetic; D006801:Humans; D056186:Metagenomics / Q000191:economics / Q000379:methods*; D011506:Proteins / Q000737:chemistry; D017385:Sequence Homology; D012984:Software; D013997:Time Factors
chemical_list: D011506:Proteins; D004247:DNA