Dynamic Smith-Waterman Algorithm: A High-Performance Grid-Enabled Application Integrated with Globus, GridSphere Portal Framework and CoG Workflow for Performing Biological Local Sequence Alignment
Md. KhairulBasharChowdhury, Tanzeem Bin Noor, Md. Rubaiyet Sadi, Md. Mahbub-ul-Alam · International Journal of Computer Applications · 2012
Smith-Waterman algorithm is one of the most significantly used algorithm and a well known approach to gain information about unknown genes and proteins for biological research.As execution time and accuracy is of great significance as handling large-scale dataset, a more reliable high-throughput and efficient parallelism can be achieved with the adaptation of grid environment.Adapting Smith-Waterman algorithm with the grid environment brings several concerns regarding fault tolerance, variability in resource performance and workload distribution, application availability etc.The work presented here aims at the development of a Dynamic Smith-Waterman algorithm metascheduler that handles all the specifications of job submission on the grid to the end user for local alignment search.Additionally a web based portal using GridSphere portal framework integrated with Globus 4 and Java Commodity Grid Kit is developed that reduces the complexity to the end users in accessing, managing and manipulating the grid resources and applications.The main contribution towards Dynamic Smith-Waterman algorithm is the reduction of the total job execution time up to 52% with accuracy up to 99.99% and better resource utilization by 40%.In addition, this work can be used as a template for the development of similar applications in future.