Power-Efficient Pipelined Multiprocessor Architecture With Parallel Trace-Back Mechanism for Multiple Pairwise Sequence Alignment

Due to the exponential growth of sequence databases, the processing of genome sequencing in real-time is a fundamental problem. Though several schemes have been developed over the years, unfortunately, they suffer from time-consumption, power-consumption, and resource-bound tradeoff issues. Another major issue concerns designing efficient architecture to perform the alignment of multiple sequences. A novel hierarchical multiprocessing architecture, designed around pipelined processing elements, is presented for multiple pairwise sequence alignment at hardware-speed. In addition to parallel intrasequence trace-back value generation, it can efficiently perform parallel intersequence computation to attain maximum utilization of processing elements. It can accomplish parallel trace-back operations to achieve massive parallelism. It consumes ${O({ni})}$ or ${O({ji})}$ clock-cycles to perform alignment operations for $j$ -nucleotide query and $i$ reference sequences of $n$ -nucleotide, instead of ${O({(n+j)i})}$ or ${O({nji})}$ clock-cycles used in state-of-the-art architectures. The entire architecture is evaluated for 16-to-512 multiple sequences of 16-to-512 nucleotides. It achieves $\approx 1.6$ to $\approx 24~\mathrm {GCUPS}$ (GCUPS: Giga cell updates per second) throughput and $\approx 5$ to $\approx 12.5~{\mathrm{ GCUPS/W}}$ power-efficiency for 16-to-64 sequences and $\approx 1.6$ to $\approx 5.6~{\mathrm{ GCUPS/W}}$ for 128-to-512 sequences. The peak throughput for 1024-nucleotide sequence is 128 GCUPS, and power-efficiency is $41~{\mathrm{ GCUPS/W}}$ . Finally, the presented architecture exhibits a gain of $\approx 2\times $ in throughput and $\approx 6\times $ in power-efficiency compared to state-of-the-art architectures.