High-speed multiple sequence alignment on a reconfigurable platform.
Progressive alignment is a widely used approach to compute multiple sequence alignments (MSAs). However, aligning several hundred sequences by popular progressive alignment tools requires hours on sequential computers. Due to the rapid growth of sequence databases biologists have to compute MSAs in a far shorter time. In this paper we present a new approach to MSA on reconfigurable hardware platforms to gain high performance at low cost. We have constructed a linear systolic array to perform pairwise sequence distance computations using dynamic programming. This results in an implementation with significant runtime savings on a standard FPGA.
Oliver
Tim
T
School of Computer Engineering, Nanyang Technological University, Singapore. tim.oliver@gmail.com
Schmidt
Bertil
B
Maskell
Douglas
D
Nathan
Darran
D
Clemens
Ralf
R
D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D003205:Computing Methodologies; D030562:Databases, Protein; D016415:Sequence Alignment / Q000295:instrumentation* / Q000379:methods*; D020539:Sequence Analysis, Protein; D012815:Signal Processing, Computer-Assisted; D012984:Software; D014584:User-Computer Interface