A lightweight BLASTP and its implementation on CUDA GPUs

Huang, Liang Tsung; Wei, Kai Cheng; Wu, Chao; Chen, Chao Yu; Wang, Jian An

doi:10.1007/s11227-020-03267-1

Cited by 6 publications

(10 citation statements)

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“…Sequence alignment is widely applied in gene prediction, analysis of the function of genes or proteins, analysis of species evolution and detection of mutation, insertion, or loss. The Smith-Waterman algorithm to perform local sequence alignment is a common method in sequence alignment [4][5][6], but it takes a long time to query large-scale datasets due to its quadratic complexity [26]. In order to improve the weakness of long runtime for the Smith-Waterman algorithm, and in response to the explosive high-dimensional growth of biologic information, the sequence analysis tool BLAST, developed by NCBI in the USA, is currently the most widely used database search algorithm.…”

Section: Blastmentioning

confidence: 99%

“…Especially the compute unified device architecture (CUDA) [22][23][24][25] has made GPU programming much easier. The main GPU optimization techniques include a reduction of bank conflict and branch divergence and enhancement of memory coalescing [26].…”

Section: Introductionmentioning

confidence: 99%

“…In recent work [26], a lightweight BLASTP has been proposed especially for those queries of lengths smaller than 512. Because the hit detection process is the most timeconsuming procedure in BLASTP and the core structure of the process is a lookup table, the lightweight BLASTP aims at designing a much smaller lookup table to increase the utilization of the query table with a lower cache miss ratio.…”

Section: Introductionmentioning

confidence: 99%

“…Experimental results show that for the first two stages the lightweight BLASTP outperforms CUDA-BLASTP with a speedup of 3.37. Moreover, a Compact BLASTP has been also proposed especially for query sequences of lengths smaller than 129 in the work [26]. The size of the lookup table can be further reduced, which is more suitable for exploiting the power of the fast but small shared memory on CUDA GPU.…”

Section: Introductionmentioning

confidence: 99%

“…In other words, the new version not only expands the service coverage for longer sequences but also provides better performance for shorter sequences supported in the original version. Therefore, the improved lightweight BLASTP proposed in this paper can fully replace the original lightweight BLASTP [26].…”

Section: Introductionmentioning

confidence: 99%

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The Design and Implementation of an Improved Lightweight BLASTP on CUDA GPU

Sun

Liu

2021

Symmetry

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In the field of computational biology, sequence alignment is a very important methodology. BLAST is a very common tool for performing sequence alignment in bioinformatics provided by National Center for Biotechnology Information (NCBI) in the USA. The BLAST server receives tens of thousands of queries every day on average. Among the procedures of BLAST, the hit detection process whose core architecture is a lookup table is the most time-consuming. In the latest work, a lightweight BLASTP on CUDA GPU with a hybrid query-index table was proposed for servicing the sequence query length shorter than 512, which effectively improved the query efficiency. According to the reported protein sequence length distribution, about 90% of sequences are equal to or smaller than 1024. In this paper, we propose an improved lightweight BLASTP to speed up the hit detection time for longer query sequences. The largest sequence is enlarged from 512 to 1024. As a result, one more bit is required to encode each sequence position. To meet the requirement, an extended hybrid query-index table (EHQIT) is proposed to accommodate three sequence positions in a four-byte table entry, making only one memory access sufficient to retrieve all the position information as long as the number of hits is equal to or smaller than three. Moreover, if there are more than three hits for a possible word, all the position information will be stored in contiguous table entries, which eliminates branch divergence and reduces memory space for pointers to overflow buffer. A square symmetric scoring matrix, Blosum62, is used to determine the relative score made by matching two characters in a sequence alignment. The experimental results show that for queries shorter than 512 our improved lightweight BLASTP outperforms the original lightweight BLASTP with speedups of 1.2 on average. When the number of hit overflows increases, the speedup can be as high as two. For queries shorter than 1024, our improved lightweight BLASTP can provide speedups ranging from 1.56 to 3.08 over the CUDA-BLAST. In short, the improved lightweight BLASTP can replace the original one because it can support a longer query sequence and provide better performance.

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