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

Abstract

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.