文章基本信息

标题：A Multi-core multithreaded parallel computation technique for DNA sequence comparison using tiling mechanism
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作者：Harshita G.Patil ; Manish Narnaware
期刊名称：International Journal of Computer Technology and Applications
电子版ISSN：2229-6093
出版年度：2012
卷号：3
期号：1
页码：125-129
出版社：Technopark Publications
摘要：This Project shows the issues involved in implementing a dynamic programming algorithm for biological sequence comparison on a general purpose parallel computing platform based on fine –grain event –driven multithreaded program execution model. Fine –grain multithreading permits efficient parallelism in this application both by taking advantage of asynchronous point-to–point synchronizations and communication with low overheads and by effectively tolerating latency through the overlapping of computation and communication. For this tiling technique can be implemented. Tiling is an important technique for extraction of parallelism. Informally, tiling consists of partitioning the iteration space into several chunks of computation called tiles (blocks) such that sequential traversal of the tiles covers the entire iteration space. The idea behind tiling is to increase the granularity of computation and decrease the amount of communication incurred between processors. This makes tiling more suitable for distributed memory architectures where communication startup costs are very high and hence frequent communication is undesirable. Our work to develop sequence-comparison mechanism and software supports the identification of sequences of DNA
关键词：Sequences alignment; dynamic programming algorithms; FASTA