Multiple Sequence Alignment Using Reconfigurable Computing

The alignment of multiple protein (or DNA) sequences is a current problem in Bioinformatics. ClustalW is themost popular heuristic algorithm for multiple sequence alignment. Pairwise alignment has exponential complexity and it is the most time-consuming part of ClustalW. This part of ClustalWwas implemented using a reconfigurable logic hard-ware solution: Hardalign. The system was evaluated using data sets of different dimensionality, and compared with a pure software version running in a embedded processor, as well as running in a desktop computer.Results indicate that such implementation is capable of accelerating significantly part of the algorithm, and this is especially important for processing large protein data sets.