RT Conference Proceedings
T1 Accelerating exhaustive pairwise metagenomic comparisons
A1 Perez-Wohlfeil, Esteban
A1 Torreño Tirado, Óscar
A1 Trelles-Salazar, Oswaldo Rogelio
K1 Genomas - Congresos
AB 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.
PB Springer, Cham
YR 2017
FD 2017-08-11
LK http://hdl.handle.net/10630/14427
UL http://hdl.handle.net/10630/14427
LA eng
NO 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.
NO Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech
DS RIUMA. Repositorio Institucional de la Universidad de Málaga
RD 20 ene 2026