Title :
Cache and energy efficient alignment of very long sequences
Author :
Chunchun Zhao;Sartaj Sahni
Author_Institution :
Department of Computer and Information Science and Engineering, University of Florida, United States
Abstract :
We develop cache and energy efficient algorithms to align very long sequences. These algorithms were evaluated experimentally on a single node of the IBM Blue Gene/Q. We were able to reduce the run time of the classical Myers and Miller linear space alignment algorithm by up to 43%; energy consumption was reduced by up to 45% on our test data.
Keywords :
"Heuristic algorithms","Computational modeling","Algorithm design and analysis","Strips","Computers","Prefetching","Approximation algorithms"
Conference_Titel :
Computational Advances in Bio and Medical Sciences (ICCABS), 2015 IEEE 5th International Conference on
DOI :
10.1109/ICCABS.2015.7344703
