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oai:riuma.uma.es:10630/144272026-02-03T12:25:56Zcom_10630_2254col_10630_37959

Perez-Wohlfeil, Esteban Torreño Tirado, Óscar Trelles-Salazar, Oswaldo Rogelio 2017-09-06T06:50:55Z 2017-09-06T06:50:55Z 2017-08-11 Pérez-Wohlfeil, E., Torreno, O., & Trelles, O. (2017, August). Accelerating Exhaustive Pairwise Metagenomic Comparisons. In International Conference on Algorithms and Architectures for Parallel Processing (pp. 611-620). Springer, Cham. http://hdl.handle.net/10630/14427 http://orcid.org/0000-0003-1554-8987 In this manuscript, we present an optimized and parallel version of our previous work IMSAME, an exhaustive gapped aligner for the pairwise and accurate comparison of metagenomes. Parallelization strategies are applied to take advantage of modern multiprocessor architectures. In addition, sequential optimizations in CPU time and memory consumption are provided. These algorithmic and computational enhancements enable IMSAME to calculate near optimal alignments which are used to directly assess similarity between metagenomes without requiring reference databases. We show that the overall efficiency of the parallel implementation is superior to 80% while retaining scalability as the number of parallel cores used increases. Moreover, we also show thats equential optimizations yield up to 8x speedup for scenarios with larger data. eng open access by-nc-nd Genomas - Congresos Accelerating exhaustive pairwise metagenomic comparisons conference output