2026-05-30T07:51:47Zhttps://riuma.uma.es/rest/oai/requestoai:riuma.uma.es:10630/144272026-02-03T12:25:56Zcom_10630_2254col_10630_37959
RIUMA. Repositorio Institucional de la Universidad de Málaga
author
Perez-Wohlfeil, Esteban
author
Torreño Tirado, Óscar
author
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
by-nc-nd
Genomas - Congresos
Accelerating exhaustive pairwise metagenomic comparisons
conference output
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URL
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File
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924d0171cc4d0e4f811c3b5d14aef024
320977
application/pdf
Accelerating_exhaustive_pairwise_metagenomic_comparisons.pdf