Abstract
As one of the most important and computationally-intensive parts in bioinformatics analysis, the Pair Hidden Markov Model (Pair-HMM) forward algorithm is widely recognized and has great potential. Therefore, it is important to accelerate the process of this algorithm. There are various approaches to accelerate Pair-HMM, especially the accelerators stemmed from the Field Programmable Gate Array (FPGA) due to the highly-customizable on-chip resources and deep pipeline potential available to the designer. In this paper, we focus on the FPGA-based accelerators for the Pair-HMM forward algorithm proposed in recent years. The non-cooperation structure, which was proposed in our previous work, is compared with the Systolic Array (SA) structure and PE ring structure in the structure characteristics, calculation mode, computational efficiency, and storage requirement. We build an analysis model to evaluate the performance of the ring structure and our non-cooperative structure. Furthermore, based on this, we provide a detailed analysis of the characteristics of structures of different accelerators and of the selection of a suitable structure for different scenarios. Based on the non-cooperative PE structure, we design a new chain topology for the accelerator. Experimental results show that our non-cooperation structure is superior to the other structures in performance and execution efficiency, and our new topology improves the performance of the accelerator. Finally, we propose some ideas about the improvement of the non-cooperative structure accelerator for future work.
Highlights
Gene sequence alignment is a process that compares the target sequence of DNA, RNA, or a protein with the reference sequence and obtains the similarity between the two gene sequences [1]
Using an analysis model we built to evaluate the performance of these Field Programmable Gate Array (FPGA)-based accelerators, we provide a detailed analysis of the characteristics of the structures of different accelerators
We built a parametric model to analyze the differences among the structures from the aspects of the calculation mode, the computational efficiency, and the storage requirement
Summary
Gene sequence alignment is a process that compares the target sequence of DNA, RNA, or a protein with the reference sequence and obtains the similarity between the two gene sequences [1]. Considering the need for throughput and performance while dealing with gene sequences with variable sizes, we designed a Pair-HMM forward algorithm accelerator with the non-cooperative PE structure in [20]. Due to the independent control of each PE, it brings the consumption of the resources of the FPGA compared with other structures Based on this detailed comparison and analysis, we propose a new idea for the topology of the accelerator.
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