A systolic array processor for biological information signal processing
ICS '91 Proceedings of the 5th international conference on Supercomputing
FPL Implementation of Systolic Sequence Alignment
Selected papers from the Second International Workshop on Field-Programmable Logic and Applications, Field-Programmable Gate Arrays: Architectures and Tools for Rapid Prototyping
FPL '02 Proceedings of the Reconfigurable Computing Is Going Mainstream, 12th International Conference on Field-Programmable Logic and Applications
Swasad: An Asic Design For High Speed Dna Sequence Matching
ASP-DAC '02 Proceedings of the 2002 Asia and South Pacific Design Automation Conference
Introduction to Bioinformatics
Introduction to Bioinformatics
Hyper customized processors for bio-sequence database scanning on FPGAs
Proceedings of the 2005 ACM/SIGDA 13th international symposium on Field-programmable gate arrays
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Local alignment of two protein sequences shows the similar regions between these proteins. Usually, a query protein sequence is aligned with several hundred thousands of protein sequences stored in databases. Since this procedure is computationally demanding, various hardware units are designed to get high quality results in a practically useful time. This paper presents efficient hardware designs that compute the local alignment scores of protein sequences. The presented designs are compared with the reference designs. All designs are implemented using ASIC and FPGA technologies. Syntheses results show that compared to the reference designs the proposed ASIC implementations achieve frequency improvements up to 250 % and hardware gains up to 40 %, and the proposed FPGA implementations achieve frequency improvements up to 29 % and hardware gains up to 48 %.