23-05-2011, 08:15 AM
Web Server for High Performance Biological Sequence Alignment Based on FPGA
An FPGA-based web server for biological sequence alignment is presented in this article. The FPGA cores used in this server are highly parameterisable, scalable, and platform-independent. Te main components of the web server are :
-an HTML–based interface
-a MySQL database for holding the user queries and results.
-a library of FPGA configurations
-a host application servicing user requests
-an FPGA coprocessor which is used for the purpose of acceleration of the sequence alignment operation.
The testing was done on the server and it achieved two orders magnitude speed-up for a pairwise protein sequence alignment application based on the Smith-Waterman algorithm. Another advantage is that the device is over 100 times energy efficient than the original web servers.
In molecular biology, the scanning the protein sequence and genome sequence is a major task. By scanning the sequences improvements are achieved in disease diagnosis, drug engineering, bio-material engineering and genetic engineering. There are heuristics based and HMM-based algorithms for the sequence alignment and they present various execution speed/accuracy tradeoffs. accurate and fast alignment algorithms need faster computer technologies. a candidate technology to solve this problem is the FPGA as they have low power consumption and high performance.
Get the report here:
http://www.mediafirefile/pmms4b8lh6p9db6...20FPGA.pdf
An FPGA-based web server for biological sequence alignment is presented in this article. The FPGA cores used in this server are highly parameterisable, scalable, and platform-independent. Te main components of the web server are :
-an HTML–based interface
-a MySQL database for holding the user queries and results.
-a library of FPGA configurations
-a host application servicing user requests
-an FPGA coprocessor which is used for the purpose of acceleration of the sequence alignment operation.
The testing was done on the server and it achieved two orders magnitude speed-up for a pairwise protein sequence alignment application based on the Smith-Waterman algorithm. Another advantage is that the device is over 100 times energy efficient than the original web servers.
In molecular biology, the scanning the protein sequence and genome sequence is a major task. By scanning the sequences improvements are achieved in disease diagnosis, drug engineering, bio-material engineering and genetic engineering. There are heuristics based and HMM-based algorithms for the sequence alignment and they present various execution speed/accuracy tradeoffs. accurate and fast alignment algorithms need faster computer technologies. a candidate technology to solve this problem is the FPGA as they have low power consumption and high performance.
Get the report here:
http://www.mediafirefile/pmms4b8lh6p9db6...20FPGA.pdf