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Bioinformatics Advance Access originally published online on May 26, 2005
Bioinformatics 2005 21(16):3431-3432; 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{at}oupjournals.org

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

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

*To whom correspondence should be addressed.

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 Pentium IV 3 GHz 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.

Contact: tim.oliver{at}pmail.ntu.edu.sg

Received on March 21, 2005; revised on April 29, 2005; accepted on May 18, 2005

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