Grid and Cooperative Computing - GCC 2004

Volume 3251 of the series Lecture Notes in Computer Science pp 777-782

Memory Efficient Pair-Wise Genome Alignment Algorithm – A Small-Scale Application with Grid Potential

  • Nova AhmedAffiliated withGeorgia State University
  • , Yi PanAffiliated withGeorgia State University
  • , Art VandenbergAffiliated withGeorgia State University

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Grid middleware infrastructure is a distributed environment suitable for many, typically large-scale, applications. An improved genome sequence alignment algorithm is presented that significantly reduces sequence matching computation time. Yet, very long sequences can still present computation challenges. A small-scale application is implemented on a shared memory system, on a cluster, and the grid-enabled cluster. Experimental results show comparable performance of the grid-enabled version, with scalability for large sequences. The grid offers application management, enables dynamic specification of parameters, and enables a choice of distributed computation nodes.


Grid computing distributed computing computational biology biological sequence alignment