An FPGA-Based Web Server for High Performance Biological Sequence Alignment

被引：2

作者：

Liu, Ying ^{[1
]}

Benkrid, Khaled ^{[1
]}

Benkrid, AbdSamad ^{[2
]}

Kasap, Server ^{[1
]}

机构：

[1] Univ Edinburgh, Inst Integrated Micro & Nano Syst, Joint Res Inst Integrated Syst, Sch Engn, Kings Bldg,Mayfield Rd, Edinburgh EH9 3J, Midlothian, Scotland

[2] Queens Univ Belfast, Sch Elect Elect Engn & Comp Sci, Belfast BT7 1NN, Antrim, North Ireland

来源：

PROCEEDINGS OF THE 2009 NASA/ESA CONFERENCE ON ADAPTIVE HARDWARE AND SYSTEMS | 2009年

关键词：

SEARCH;

D O I：

10.1109/AHS.2009.59

中图分类号：

TP301 [理论、方法];

学科分类号：

081202 ;

摘要：

This paper presents the design and implementation of the FPGA-based web server for biological sequence alignment. Central to this web-server is a set of highly parameterisable, scalable, and platform-independent FPGA cores for biological sequence alignment. The web server consists of an HTML based interface, a MySQL database which holds user queries and results, a set of biological databases, a library of FPGA configurations, a host application servicing user requests, and an FPGA coprocessor for the acceleration of the sequence alignment operation. The paper presents a real implementation of this server on an HP ProLiant DL145 server with a Celoxica RCHTX FPGA board. Compared to an optimized pure software implementation, our FPGA-based web server achieved a two order of magnitude speed-up for a pairwise protein sequence alignment application based on the Smith-Waterman algorithm. The FPGA-based implementation has the added advantage of being over 100x more energy-efficient.

引用

页码：361 / +

页数：3

共 50 条

[21] A High-performance FPGA-based Accelerator for Gradient Compression
Ren, Qingqing
Zhu, Shuyong
Meng, Xuying
Zhang, Yujun
DCC 2022: 2022 DATA COMPRESSION CONFERENCE (DCC), 2022, : 429 - 438
[22] High performance computing engines for the FPGA-based simulation of the ULM
Ould-Bachir, Tarek
Chalangar, Hossein
Sheshyekani, Keyhan
Mahseredjian, Jean
ELECTRIC POWER SYSTEMS RESEARCH, 2021, 190
[23] High Performance FPGA-based Post Quantum Cryptography Implementations
Ni, Ziying
Khalid, Ayesha
O'Neill, Maire
2022 32ND INTERNATIONAL CONFERENCE ON FIELD-PROGRAMMABLE LOGIC AND APPLICATIONS, FPL, 2022, : 456 - 457
[24] FPGA-Based High-Performance Network Impairment Emulator
Duan, Dexuan
Wang, Xinshuo
Li, Lin
Liu, Lei
ELECTRONICS, 2024, 13 (24):
[25] High level performance metrics for FPGA-based multiprocessor systems
Beltran, Marta
Guzman, Antonio
Sevillano, Fernando
PERFORMANCE EVALUATION, 2010, 67 (06) : 417 - 431
[26] High-performance FPGA-based implementation of Kalman filter
Lee, CR
Salcic, Z
MICROPROCESSORS AND MICROSYSTEMS, 1997, 21 (04) : 257 - 265
[27] FPGA-based architecture for motion sequence extraction
Diaz, J.
Ros, E.
Mota, S.
Rodriguez-Gomez, R.
INTERNATIONAL JOURNAL OF ELECTRONICS, 2007, 94 (05) : 435 - 450
[28] High performance Web server based on the ASPED model
Lei, Y.C.
Li, G.J.
Jisuanji Yanjiu yu Fazhan/Computer Research and Development, 2001, 38 (07):
[29] An Optimized and Low-cost FPGA-based DNA Sequence Alignment - A Step towards Personal Genomics
Shah, Hurmat Ali
Hasan, Laiq
Ahmad, Nasir
2013 35TH ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY (EMBC), 2013, : 2696 - 2699
[30] Design and Implementation of an FPGA-based Core for Gapped BLAST Sequence Alignment with the Two-Hit Method
Kasap, Server
Benkrid, Khaled
Liu, Ying
ENGINEERING LETTERS, 2008, 16 (03)

← 1 2 3 4 5 →