Parallel Implementation & Performance Evaluation of BLAST Algorithm on LINUX Cluster

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dc.contributor.advisorGupta, O.P.
dc.contributor.authorDhankher, Nisha
dc.date.accessioned2016-10-05T13:53:16Z
dc.date.available2016-10-05T13:53:16Z
dc.date.issued2014
dc.description.abstractBLAST is an efficient heuristic based algorithm, used for calculating local alignment between biological sequences. Due to exponential growth in the size of genomic databases, traditional techniques of sequence search proved to be slow. To address the above problem, an open source and parallel version of BLAST called mpiBLAST was developed by the programmers. In mpiBLAST, the master process distributes the database fragments among worker nodes to compute the sequence search in parallel. As merging and writing of the results is done sequentially by the master process, it would create performance bottleneck with increasing number of processors and varying database sizes. To handle this high nonsearch overhead, mpiBLAST-PIO was introduced. This study describes the optimized and extended version of mpiBLAST called mpiBLAST-PIO. The goal of this research was to investigate the performance of parallel implementation of BLAST in comparison to sequential NCBI-BLAST by measuring Speedup and efficiency on HPC Platform using Infiniband. Different options of mpiBLAST-PIO were activated that helped in understanding the optimal parameters for achieving highly scalable parallel BLAST implementation. The results found that parallel-writing of the results, can evolve as an efficient solution when high-performance parallel file system is available.en_US
dc.identifier.urihttp://krishikosh.egranth.ac.in/handle/1/80006
dc.language.isoenen_US
dc.publisherPunjab Agricultural University, Ludhianaen_US
dc.subComputer Science and Engineering
dc.subjectParallel & Distributed Computingen_US
dc.subjectInformation Technologyen_US
dc.subjectBioinformaticsen_US
dc.subjectBLASTen_US
dc.subjectLINUX Clusteren_US
dc.these.typeM.Tech
dc.titleParallel Implementation & Performance Evaluation of BLAST Algorithm on LINUX Clusteren_US
dc.typeThesisen_US
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