title: Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW.
abstract: 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.
authors.affiliation: School of Computer Engineering, Nanyang Technological University, Singapore. tim.oliver@pmail.ntu.edu.sg
authors.forename: Tim
authors.initials: T
authors.lastname: Oliver
authors.forename: Bertil
authors.initials: B
authors.lastname: Schmidt
authors.forename: Darran
authors.initials: D
authors.lastname: Nathan
authors.forename: Ralf
authors.initials: R
authors.lastname: Clemens
authors.forename: Douglas
authors.initials: D
authors.lastname: Maskell
mesh_terms: 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