https://scholars.lib.ntu.edu.tw/handle/123456789/607360
標題: | A memory-efficient accelerator for DNA sequence alignment with two-piece affine gap tracebacks | 作者: | Wu J.-P Lin Y.-C Wu Y.-W Hsieh S.-W Tai C.-H Lu Y.-C. YI-CHANG LU |
關鍵字: | Sequence alignment;Smith-Waterman;Traceback;Two-piece affine gap;Decoding;DNA sequences;DNA sequence alignments;Gap model;Memory efficient;Memory usage;Pairwise alignment;Penalty function;Speed up;Dynamic programming | 公開日期: | 2021 | 卷: | 2021-May | 來源出版物: | Proceedings - IEEE International Symposium on Circuits and Systems | 摘要: | Previously, dynamic-programming-based DNA sequence aligners were mostly implemented with a penalty function of the one-piece affine gap model. When aligning sequences with longer gaps, the two-piece affine gap model provides better results at the cost of memory usage, which becomes an issue especially for aligners with memory-hungry traceback capabilities. In this paper, we design a memory-efficient scheme for traceback recording with the two-piece penalty scoring, so that the aligner can be realized on an ASIC. Our design is implemented with TSMC 40nm technology, and the proposed aligner can speed up pairwise alignment by 71× compared to the CPU approach. ? 2021 IEEE |
URI: | https://www.scopus.com/inward/record.uri?eid=2-s2.0-85109037307&doi=10.1109%2fISCAS51556.2021.09401771&partnerID=40&md5=77106ae34d2faf49268f18cf711ab154 https://scholars.lib.ntu.edu.tw/handle/123456789/607360 |
ISSN: | 02714310 | DOI: | 10.1109/ISCAS51556.2021.09401771 |
顯示於: | 電機工程學系 |
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