Grid-Enabled BLASTZ: Application to Comparative Genomics

Authors:
Chunxi Chen;Jagath C. Rajapakse
Affiliations:
BioInformatics Research Center, School of Computer Engineering, Nanyang Technological University, Singapore, Singapore;BioInformatics Research Center, School of Computer Engineering, Nanyang Technological University, Singapore, Singapore and Singapore-MIT Alliance, Singapore, Singapore
Venue:
Journal of VLSI Signal Processing Systems
Year:
2007

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Abstract

BLASTZ is a sequence alignment tool designed mainly for aligning neutrally evolved bio-sequences and has been the choice for aligning noncoding sequences. However, its running time is impractical for high throughput alignment of long sequences, for example, for the alignment of human and mouse genomes. In order to improve the performance and efficiency for alignment at genome scale, BLASTZ was implemented using the GLOBUS toolkit on a computing grid. A dynamic load balancing technique was introduced to achieve enhanced performance on a grid which consists of sources of heterogeneous characteristics, such as resources of different computational powers. The robustness of the implementation to disturbances due to other processes on the grid is demonstrated.