Chen, Chuan YuChuan YuChenHuang, Shih HaoShih HaoHuangYI-CHANG LU2023-07-172023-07-172022-01-019781665469173https://scholars.lib.ntu.edu.tw/handle/123456789/633774Sequence alignment plays an important role in bioinformatics. In this paper, we propose an application-specific integrated circuit (ASIC) design for the pairwise sequence alignment using Levenshtein distance based on the Myers bit-vector algorithm. We also design an accelerator for the divide-and-conquer-based Hirschberg's algorithm to reduce memory usage, so that the on-chip traceback function can be supported. The hardware is implemented with TSMC 40 nm technology and the maximum input sequence size of the aligner is 10,240 × 5,242,880 bps. Our hardware accelerator can achieve 3,992 GCUPS, which speeds up the pairwise alignment by 147× when compared with the software counterpart for the sequences of 90% similarity.divide and conquer | dynamic programming | hardware acceleration | pair-wise alignment | tracebackconference paper10.1109/BioCAS54905.2022.99485602-s2.0-85142919617https://api.elsevier.com/content/abstract/scopus_id/85142919617