Ruei-Ting Chien, Yi-Lun Liao, Chien-An Wang, Yu-Cheng Li, Yi-Chang Lu
{"title":"Three-Dimensional Dynamic Programming Accelerator for Multiple Sequence Alignment","authors":"Ruei-Ting Chien, Yi-Lun Liao, Chien-An Wang, Yu-Cheng Li, Yi-Chang Lu","doi":"10.1109/NORCHIP.2018.8573523","DOIUrl":"https://doi.org/10.1109/NORCHIP.2018.8573523","url":null,"abstract":"Three sequence alignment can be used to improve the accuracy of multiple sequence alignment in genomics. In this paper, we design a hardware accelerator for three-dimensional dynamic programming algorithm of three sequence alignment. By utilizing parallel processing elements, our design can find the optimal alignment scores in a shorter time than that required by software. In addition, we propose a memory-efficient slicing method for three-dimensional dynamic programming in order to process sequences of longer lengths. The hardware accelerator is implemented on both FPGA and ASIC. The ASIC implementation using TSMC 40nm technology can achieve at least 160× speedup over the software implementation.","PeriodicalId":152077,"journal":{"name":"2018 IEEE Nordic Circuits and Systems Conference (NORCAS): NORCHIP and International Symposium of System-on-Chip (SoC)","volume":"43 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127014005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
O. Schrape, A. Balashov, A. Simevski, Carlos Benito, M. Krstic
{"title":"Master-Clone Placement with Individual Clock Tree Implementation – a Case on Physical Chip Design","authors":"O. Schrape, A. Balashov, A. Simevski, Carlos Benito, M. Krstic","doi":"10.1109/NORCHIP.2018.8573453","DOIUrl":"https://doi.org/10.1109/NORCHIP.2018.8573453","url":null,"abstract":"A hybrid design approach of the hierarchical physical implementation design flow is presented and demonstrated on a fault-tolerant low-power multiprocessor system. The proposed flow allows to implement selected submodules in parallel with contrary requirements such as identical placement and individual block implementation. The overall system contains four Leon2 cores and communicates via the Waterbear framework and supports Adaptive Voltage Scaling (AVS) functionality. Three of the processor core variants are derived from the first baseline reference core but implemented individually at block level based on their clock tree specification. The chip is prepared for space applications and designed with triple modular redundancy (TMR) for control parts. The low-power performance is enabled by contemporary power and clock management control. An ASIC is fabricated in a low-power $0.13 mu mathrm{m}$ BiCMOS technology process node.","PeriodicalId":152077,"journal":{"name":"2018 IEEE Nordic Circuits and Systems Conference (NORCAS): NORCHIP and International Symposium of System-on-Chip (SoC)","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126875064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}