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Open Access Technical Note

DOPA: GPU-based protein alignment using database and memory access optimizations

Laiq Hasan*, Marijn Kentie and Zaid Al-Ars

Author Affiliations

Computer Engineering Laboratory, Faculty of Electrical Engineering Mathematics and Computer Science (EEMCS), Delft University of Technology (TU Delft), Mekelweg 4, 2628 CD, Delft, The Netherlands

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BMC Research Notes 2011, 4:261  doi:10.1186/1756-0500-4-261

Published: 28 July 2011



Smith-Waterman (S-W) algorithm is an optimal sequence alignment method for biological databases, but its computational complexity makes it too slow for practical purposes. Heuristics based approximate methods like FASTA and BLAST provide faster solutions but at the cost of reduced accuracy. Also, the expanding volume and varying lengths of sequences necessitate performance efficient restructuring of these databases. Thus to come up with an accurate and fast solution, it is highly desired to speed up the S-W algorithm.


This paper presents a high performance protein sequence alignment implementation for Graphics Processing Units (GPUs). The new implementation improves performance by optimizing the database organization and reducing the number of memory accesses to eliminate bandwidth bottlenecks. The implementation is called Database Optimized Protein Alignment (DOPA) and it achieves a performance of 21.4 Giga Cell Updates Per Second (GCUPS), which is 1.13 times better than the fastest GPU implementation to date.


In the new GPU-based implementation for protein sequence alignment (DOPA), the database is organized in equal length sequence sets. This equally distributes the workload among all the threads on the GPU's multiprocessors. The result is an improved performance which is better than the fastest available GPU implementation.