Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW.
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.
Oliver
Tim
T
School of Computer Engineering, Nanyang Technological University, Singapore. tim.oliver@pmail.ntu.edu.sg
Schmidt
Bertil
B
Nathan
Darran
D
Clemens
Ralf
R
Maskell
Douglas
D
D003201:Computers; D030562:Databases, Protein; D004867:Equipment Design; D019544:Equipment Failure Analysis; D016415:Sequence Alignment / Q000295:instrumentation* / Q000379:methods; D020539:Sequence Analysis, Protein / Q000295:instrumentation* / Q000379:methods; D012815:Signal Processing, Computer-Assisted / Q000295:instrumentation*; D012984:Software; D014584:User-Computer Interface