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MASA: a multi-platform architecture for sequence aligners with block pruning

Author
De Sandes, E.; Miranda, G.; Martorell, X.; Ayguade, E.; Teodoro, G.; de Melo, A.
Type of activity
Journal article
Journal
ACM Transactions on Parallel Computing
Date of publication
2016-03-01
Volume
2
Number
4
First page
28:1
Last page
28:31
DOI
https://doi.org/10.1145/2858656 Open in new window
Project funding
SEV-2011-00067
TIN2012-34557
Repository
http://hdl.handle.net/2117/99739 Open in new window
URL
http://dl.acm.org/citation.cfm?id=2858656 Open in new window
Abstract
Biological sequence alignment is a very popular application in Bioinformatics used routinely worldwide. Many implementations of biological sequence alignment algorithms have been proposed for multicores, GPUs, FPGAs and CellBEs. These implementations are platform-specific and porting them to other systems requires considerable programming effort. This paper proposes and evaluates MASA, a flexible and customizable software architecture that enables the execution of biological sequence alignment a...
Citation
De Sandes, E., Miranda, G., Martorell, X., Ayguade, E., Teodoro, G., de Melo, A. MASA: a multi-platform architecture for sequence aligners with block pruning. "ACM Transactions on Parallel Computing", 1 Març 2016, vol. 2, núm. 4, p. 28:1-28:31.
Keywords
Biological Sequence Alignment, GPU, Intel Phi, Parallel Algorithms, multicores
Group of research
CAP - High Performace Computing Group

Participants

  • De Sandes, Edans  (author)
  • Miranda, Guillermo  (author)
  • Martorell, Xavier  (author)
  • Ayguade Parra, Eduard  (author)
  • Teodoro, George  (author)
  • de Melo, Alba  (author)