An FPGA-based web server for high performance biological sequence alignment

Ying Liu; Khaled Benkrid; AbdSamad Benkrid; S. Kasap

doi:10.1109/AHS.2009.59

An FPGA-based web server for high performance biological sequence alignment

Ying Liu, Khaled Benkrid, AbdSamad Benkrid, S. Kasap

Research output: Chapter in Book/Report/Conference proceeding › Conference proceeding › peer-review

15 Citations (Scopus)

Abstract

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

Original language	English
Title of host publication	Proceedings - 2009 NASA/ESA Conference on Adaptive Hardware and Systems, AHS 2009
Publisher	IEEE
Pages	361-368
Number of pages	8
ISBN (Print)	978-0-7695-3714-6
DOIs	https://doi.org/10.1109/AHS.2009.59
Publication status	Published - 10 Nov 2009
Externally published	Yes
Event	2009 NASA/ESA Conference on Adaptive Hardware and Systems - San Francisco, United States Duration: 29 Jul 2009 → 1 Aug 2009

Conference

Conference	2009 NASA/ESA Conference on Adaptive Hardware and Systems
Country/Territory	United States
City	San Francisco
Period	29/07/09 → 1/08/09

Access to Document

10.1109/AHS.2009.59

Cite this

Liu, Y, Benkrid, K, Benkrid, A & Kasap, S 2009, An FPGA-based web server for high performance biological sequence alignment. in Proceedings - 2009 NASA/ESA Conference on Adaptive Hardware and Systems, AHS 2009. IEEE, pp. 361-368, 2009 NASA/ESA Conference on Adaptive Hardware and Systems, San Francisco, California, United States, 29/07/09. https://doi.org/10.1109/AHS.2009.59

@inproceedings{bf522280ab1643fc8a19360036a7ef3b,

title = "An FPGA-based web server for high performance biological sequence alignment",

abstract = "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",

author = "Ying Liu and Khaled Benkrid and AbdSamad Benkrid and S. Kasap",

year = "2009",

month = nov,

day = "10",

doi = "10.1109/AHS.2009.59",

language = "English",

isbn = "978-0-7695-3714-6",

pages = "361--368",

booktitle = "Proceedings - 2009 NASA/ESA Conference on Adaptive Hardware and Systems, AHS 2009",

publisher = "IEEE",

address = "United States",

note = "2009 NASA/ESA Conference on Adaptive Hardware and Systems ; Conference date: 29-07-2009 Through 01-08-2009",

}

TY - GEN

T1 - An FPGA-based web server for high performance biological sequence alignment

AU - Liu, Ying

AU - Benkrid, Khaled

AU - Benkrid, AbdSamad

AU - Kasap, S.

PY - 2009/11/10

Y1 - 2009/11/10

N2 - 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

AB - 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

UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-72849106355&partnerID=MN8TOARS

UR - https://www.scopus.com/pages/publications/72849106355

U2 - 10.1109/AHS.2009.59

DO - 10.1109/AHS.2009.59

M3 - Conference proceeding

SN - 978-0-7695-3714-6

SP - 361

EP - 368

BT - Proceedings - 2009 NASA/ESA Conference on Adaptive Hardware and Systems, AHS 2009

PB - IEEE

T2 - 2009 NASA/ESA Conference on Adaptive Hardware and Systems

Y2 - 29 July 2009 through 1 August 2009

ER -

An FPGA-based web server for high performance biological sequence alignment

Abstract

Conference

Access to Document

Other files and links

Fingerprint

Cite this