High performance and resource efficient biological sequence alignment

Laiq Hasan; Zaid Al-Ars; Mottaqiallah Taouil

doi:10.1109/IEMBS.2010.5626740

High performance and resource efficient biological sequence alignment

Annu Int Conf IEEE Eng Med Biol Soc. 2010:2010:1767-70. doi: 10.1109/IEMBS.2010.5626740.

Authors

Laiq Hasan¹, Zaid Al-Ars, Mottaqiallah Taouil

Affiliation

¹ Computer Engineering Laboratory, Delft University of Technology, Mekelweg 4, 2628 CD, The Netherlands. L.HASAN@TUDELFT.NL

PMID: 21096417
DOI: 10.1109/IEMBS.2010.5626740

Abstract

In this paper, we present a novel method based on hardware partitioning to reduce the execution time and improve the resource utilization of biological sequence align- ment, resulting in a higher performance as compared to conventional approaches. The paper shows that the method reduces the execution time and improves the resource utilization up to 33.3%. Further, equations are derived, showing the general trend of execution time reduction, resource utilization improvement and hence performance enhancement.

MeSH terms

Algorithms*
Pattern Recognition, Automated / methods*
Sequence Alignment / methods*
Sequence Analysis / methods*