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Bioinformatics Advance Access published online on May 26, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti508
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received March 21, 2005
Revised April 29, 2005
Accepted May 18, 2005

Applications note

Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW

Tim Oliver 1*, Bertil Schmidt 1, Darran Nathan 2, Ralf Clemens 2, and Douglas Maskell 1

1 School of Computer Engineering, Nanyang Technological University, Singapore
2 Project Proteus, School of Engineering, Ngee Ann Polytechnic, Singapore

* To whom correspondence should be addressed.
Tim Oliver, E-mail: tim.oliver{at}pmail.ntu.edu.sg


  Abstract

Summary: Aligning hundreds of sequences using progressive alignment tools such as ClustalW requires several hours on state-of-the-art workstations. We present a new approach to compute multiple sequence alignments in far shorter time using reconfigurable hardware. This results in an implementation of ClustalW with significant runtime savings on a standard off-the-shelf FPGA.

Availability: An online server for ClustalW running on a Pentium4 3GHz with a Xilinx XC2V6000 FPGA PCI-board is available at: http://beta.projectproteus.org. The PE hardware design in Verilog HDL is available on request from the first author.


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