Abstract
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.
This work was partially supported by the Brazilian National Research Council – CNPq, under research grants no. 305720/2004-0 and 506479/2004-8.
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Lima, C.R.E., Lopes, H.S., Moroz, M.R., Menezes, R.M. (2007). Multiple Sequence Alignment Using Reconfigurable Computing. In: Diniz, P.C., Marques, E., Bertels, K., Fernandes, M.M., Cardoso, J.M.P. (eds) Reconfigurable Computing: Architectures, Tools and Applications. ARC 2007. Lecture Notes in Computer Science, vol 4419. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-71431-6_37
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DOI: https://doi.org/10.1007/978-3-540-71431-6_37
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