Multiple Sequence Alignment Using Reconfigurable Computing

The alignment of multiple protein (or DNA) sequences is a current problem in Bioinformatics. ClustalW is the most 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 ClustalW was implemented using a reconfigurable logic hardware 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.

• Type: Conference
• Year: 2007
• Where: ARC
• Authors: Carlos R. Erig Lima, Heitor S. Lopes, Maiko R. Moroz, Ramon M. Menezes
• Keywords: ARC 2007, ClustalW, Hardware, Multiple Sequence Alignment, Popular Heuristic Algorithm