Rapid multiple protein sequence search by parallel and heterogeneous computation

Li, Jiefu1; Wang, Ziyuan2; Fan, Xuwei2; Yao, Ruijie3; Zhang, Guoqing1,4; Fan, Rui2; Wang, Zefeng1,4,5

2024-03-29

10.1093/bioinformatics/btae151

BIOINFORMATICS   影响因子和分区

1367-4803

1367-4811

Motivation Protein sequence database search and multiple sequence alignment generation is a fundamental task in many bioinformatics analyses. As the data volume of sequences continues to grow rapidly, there is an increasing need for efficient and scalable multiple sequence query algorithms for super-large databases without expensive time and computational costs.Results We introduce Chorus, a novel protein sequence query system that leverages parallel model and heterogeneous computation architecture to enable users to query thousands of protein sequences concurrently against large protein databases on a desktop workstation. Chorus achieves over 100x speedup over BLASTP without sacrificing sensitivity. We demonstrate the utility of Chorus through a case study of analyzing a similar to 1.5-TB large-scale metagenomic datasets for novel CRISPR-Cas protein discovery within 30 min.Availability and implementation Chorus is open-source and its code repository is available at https://github.com/Bio-Acc/Chorus.

SCI

英语

通讯

Strategic Priority Research Program of Chinese Academy of Sciences (CAS)["XDC01000000","XDB38040100"] ; National Natural Science Foundation of China (NSFC)["31730110","91940303","31661143031"] ; Science and Technology Commission of Shanghai Municipality[18XD1404400] ; National Key Research and Development Program of China[2018YFA0107602] ; ShanghaiTech University[2017F0203-000-05] ; GHfund A["ghfund202202013878","ghfund202302012917"]

Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics

Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability

WOS:001203339000002

OXFORD UNIV PRESS

BIOLOGY & BIOCHEMISTRY

Web of Science

1.Chinese Acad Sci, Univ Chinese Acad Sci, Shanghai Inst Nutr & Hlth, CAS Key Lab Computat Biol, 320 Yueyang Rd, Shanghai 200031, Peoples R China
2.ShanghaiTech Univ, Sch Informat Sci & Technol, 393 Middle Huaxia Rd, Shanghai 201210, Peoples R China
3.Chinese Acad Sci, Inst Intelligent Comp Technol, 88 Jinjihu Ave, Suzhou 215000, Jiangsu, Peoples R China
4.Chinese Acad Sci, Univ Chinese Acad Sci, Shanghai Inst Nutr & Hlth, Biomed Big Data Ctr, 320 Yueyang Rd, Shanghai 200031, Peoples R China
5.Southern Univ Sci & Technol, Sch Life Sci, 1088 Xueyuan Ave, Shenzhen 518055, Guangdong, Peoples R China

Li, Jiefu,Wang, Ziyuan,Fan, Xuwei,et al. Rapid multiple protein sequence search by parallel and heterogeneous computation[J]. BIOINFORMATICS,2024,40(4).

Li, Jiefu.,Wang, Ziyuan.,Fan, Xuwei.,Yao, Ruijie.,Zhang, Guoqing.,...&Wang, Zefeng.(2024).Rapid multiple protein sequence search by parallel and heterogeneous computation.BIOINFORMATICS,40(4).

Li, Jiefu,et al."Rapid multiple protein sequence search by parallel and heterogeneous computation".BIOINFORMATICS 40.4(2024).