A parallel approach of COFFEE objective function to multiple sequence alignment
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2015-09-21
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Zafalon, G. F.D. [UNESP]
Visotaky, J. M.V. [UNESP]
Amorim, A. R. [UNESP]
ValĂȘncio, C. R. [UNESP]
Neves, L. A. [UNESP]
De Souza, R. C.G. [UNESP]
Machado, J. M. [UNESP]
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The computational tools to assist genomic analyzes show even more necessary due to fast increasing of data amount available. With high computational costs of deterministic algorithms for sequence alignments, many works concentrate their efforts in the development of heuristic approaches to multiple sequence alignments. However, the selection of an approach, which offers solutions with good biological significance and feasible execution time, is a great challenge. Thus, this work aims to show the parallelization of the processing steps of MSA-GA tool using multithread paradigm in the execution of COFFEE objective function. The standard objective function implemented in the tool is the Weighted Sum of Pairs (WSP), which produces some distortions in the final alignments when sequences sets with low similarity are aligned. Then, in studies previously performed we implemented the COFFEE objective function in the tool to smooth these distortions. Although the nature of COFFEE objective function implies in the increasing of execution time, this approach presents points, which can be executed in parallel. With the improvements implemented in this work, we can verify the execution time of new approach is 24% faster than the sequential approach with COFFEE. Moreover, the COFFEE multithreaded approach is more efficient than WSP, because besides it is slightly fast, its biological results are better.
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Journal of Physics: Conference Series, v. 633, n. 1, 2015.