nBLAST-JC: An accelerated deployment of nucleotide BLAST on high-performance cluster
BLAST is the most practiced algorithm to perform the task of sequence alignment. To cope with the voluminous growth in molecular data and reduce processing time, several accelerated versions of BLAST have been proposed by researchers. In this paper, an expeditious design of nucleotide BLAST named nB...
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| Language: | English |
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Elsevier
2025-05-01
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| Series: | Heliyon |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2405844025002464 |
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| author | Sita Rani Aman Kataria O.P. Gupta Pankaj Bhambri Hong Min |
| author_facet | Sita Rani Aman Kataria O.P. Gupta Pankaj Bhambri Hong Min |
| author_sort | Sita Rani |
| collection | DOAJ |
| description | BLAST is the most practiced algorithm to perform the task of sequence alignment. To cope with the voluminous growth in molecular data and reduce processing time, several accelerated versions of BLAST have been proposed by researchers. In this paper, an expeditious design of nucleotide BLAST named nBLAST-JC for a high-performance cluster (HPC) is proposed. The proposed algorithm is implemented on the Hadoop framework using JCuda. It can run multiple query sequences in parallel. The proposed nBLAST-JC gave a speed-up ranging from 7.1 × to 9 × in comparison to HS-BLASN and 1.8 × to 2.3 × in comparison to G-BLASTN (‘blastn’ mode). This algorithm is highly scalable for huge-sized databases due to the fundamental characteristics of the Hadoop framework. The performance of nBLAST-JC can be further enhanced using available CPU cores along with the GPU of each client node. The reliability of the proposed model can further be improved using a two-server approach. |
| format | Article |
| id | doaj-art-da63c92e58de4bae9a883a5da6968867 |
| institution | OA Journals |
| issn | 2405-8440 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Heliyon |
| spelling | doaj-art-da63c92e58de4bae9a883a5da69688672025-08-20T02:02:17ZengElsevierHeliyon2405-84402025-05-011110e4186610.1016/j.heliyon.2025.e41866nBLAST-JC: An accelerated deployment of nucleotide BLAST on high-performance clusterSita Rani0Aman Kataria1O.P. Gupta2Pankaj Bhambri3Hong Min4Department of Computer Science & Engineering, Guru Nanak Dev Engineering College, Ludhiana, 141006, Punjab, IndiaUniversity Centre for Research and Development, Chandigarh University, Gharuan, Mohali, 140413, IndiaAssociate Director IT, Punjab Agricultural University, Ludhiana, 141004, Punjab, IndiaDepartment of Information Technology, Guru Nanak Dev Engineering College, Ludhiana, 141006, Punjab, IndiaSchool of Computing, Gachon University, 1342 Seongnamdaero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, Republic of Korea; Corresponding author.BLAST is the most practiced algorithm to perform the task of sequence alignment. To cope with the voluminous growth in molecular data and reduce processing time, several accelerated versions of BLAST have been proposed by researchers. In this paper, an expeditious design of nucleotide BLAST named nBLAST-JC for a high-performance cluster (HPC) is proposed. The proposed algorithm is implemented on the Hadoop framework using JCuda. It can run multiple query sequences in parallel. The proposed nBLAST-JC gave a speed-up ranging from 7.1 × to 9 × in comparison to HS-BLASN and 1.8 × to 2.3 × in comparison to G-BLASTN (‘blastn’ mode). This algorithm is highly scalable for huge-sized databases due to the fundamental characteristics of the Hadoop framework. The performance of nBLAST-JC can be further enhanced using available CPU cores along with the GPU of each client node. The reliability of the proposed model can further be improved using a two-server approach.http://www.sciencedirect.com/science/article/pii/S2405844025002464Basic local alignment search tool (BLAST)Compute unified device architecture (CUDA)HadoopHigh-performance cluster (HPC)JCudaSequence alignment |
| spellingShingle | Sita Rani Aman Kataria O.P. Gupta Pankaj Bhambri Hong Min nBLAST-JC: An accelerated deployment of nucleotide BLAST on high-performance cluster Heliyon Basic local alignment search tool (BLAST) Compute unified device architecture (CUDA) Hadoop High-performance cluster (HPC) JCuda Sequence alignment |
| title | nBLAST-JC: An accelerated deployment of nucleotide BLAST on high-performance cluster |
| title_full | nBLAST-JC: An accelerated deployment of nucleotide BLAST on high-performance cluster |
| title_fullStr | nBLAST-JC: An accelerated deployment of nucleotide BLAST on high-performance cluster |
| title_full_unstemmed | nBLAST-JC: An accelerated deployment of nucleotide BLAST on high-performance cluster |
| title_short | nBLAST-JC: An accelerated deployment of nucleotide BLAST on high-performance cluster |
| title_sort | nblast jc an accelerated deployment of nucleotide blast on high performance cluster |
| topic | Basic local alignment search tool (BLAST) Compute unified device architecture (CUDA) Hadoop High-performance cluster (HPC) JCuda Sequence alignment |
| url | http://www.sciencedirect.com/science/article/pii/S2405844025002464 |
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