Analysing the performance of personal computers based on Intel microprocessors for sequence aligning bioinformatics applications

  • Authors:

  • Pradeep S. Nair;Eugene B. John

  • Affiliations:

  • Department of Electrical and Computer Engineering, University of Texas, San Antonio, TX 78249, USA.;Department of Electrical and Computer Engineering, University of Texas, San Antonio, TX 78249, USA

  • Venue:
  • International Journal of Bioinformatics Research and Applications
  • Year:
  • 2007

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Abstract

Aligning specific sequences against a very large number of other sequences is a central aspect of bioinformatics. With the widespread availability of personal computers in biology laboratories, sequence alignment is now often performed locally. This makes it necessary to analyse the performance of personal computers for sequence aligning bioinformatics benchmarks. In this paper, we analyse the performance of a personal computer for the popular BLAST and FASTA sequence alignment suites. Results indicate that these benchmarks have a large number of recurring operations and use memory operations extensively. It seems that the performance can be improved with a bigger L1-cache.