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We expose the implementation challenges to sustaining acceleration speedups on FPGAs as the size of the data set to be processed scales. We examine the implementation of an FPGA platform for the processing of gigabyte scale biological sequences, and illustrate the significant design changes that must be made to achieve a successful implementation. In doing so, we demonstrate that conventional accelerator...
Sequence alignment is a very important problem in Bioinformatics since it is very useful to discover relationships among biological sequences. In this article we propose a new sequence alignment algorithm that is able to identify sequence similarities in linear space. Our solution is capable of using several parameters specifying in which conditions a given residue can be aligned. This decision is...
Multiple sequence alignment (MSA) is an important problem in Bioinformatics since it is often used to identify evolutionary relationships and predict secondary/tertiary structure, among others. MSAs are usually scored with the Sum-of-Pairs (SP) function and the exact SP MSA is known to be NP-Hard. Therefore, heuristic methods are used to solve this problem. In this paper, we propose and evaluate a...
The recent and astonishing accomplishments in the field of Genomics would not have been possible without the techniques, algorithms, and tools developed in Bioinformatics. Biological sequence comparison is an important operation in Bioinformatics because it is used to determine how similar two sequences are. As a result of this operation, one or more alignments are produced. DIALIGN is an exact algorithm...
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