Reconfigurable Computing IP Cores for Multiple Sequence Alignment.

Multiple Sequence Alignment (MSA) is a principal tool in computational molecular biology. MSA is considered to be a very challenging problem as many software implementations suffer from quadratic time performance. Two of the best known MSA algorithms, which offer high accuracy and great speed, are T-Coffee and MAFFT. Reconfigurable technology provides a dramatic reduction of execution time by taking advantage of high parallelism. It also allows for different problem sizing solutions within a generic intellectual property (IP) core. This paper presents the implementation of MAFFT and T-Coffee algorithms on present-day Field Programmable Gate Arrays (FPGAs). The performance of the FPGA systems is compared against software implementations, concluding that the parallelism of reconfigurable technology can offer significant computational power to the bioinformatics community.