Abstract
Multiple sequence alignment (MSA), used in biocomputing to study similarities between different genomic sequences, is known to require important memory and computation resources. Determining the efficient amount of resources to allocate is important to avoid waste of them, thus reducing the economical costs required in running for example a specific cloud instance. The pairwise alignment is the initial key step of the MSA problem, which will compute all pair alignments needed. We present a method to determine the optimal amount of memory and computation resources to allocate by the pairwise alignment, and we will validate it through a set of experimental results for different possible inputs. These allow us to determine the best parameters to configure the applications in order to use effectively the available resources of a given system.
This work was supported by the MEyC-Spain under contract TIN 2011-28689-C02-02 and Consolider CSD2007-0050. The CUR of DIUE of GENCAT and the European Social Fund.
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Montañola, A., Roig, C., Hernández, P. (2014). Optimizing Multiple Pairwise Alignment of Genomic Sequences in Multicore Clusters. In: Saez-Rodriguez, J., Rocha, M., Fdez-Riverola, F., De Paz Santana, J. (eds) 8th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2014). Advances in Intelligent Systems and Computing, vol 294. Springer, Cham. https://doi.org/10.1007/978-3-319-07581-5_15
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DOI: https://doi.org/10.1007/978-3-319-07581-5_15
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