Dna Compressed and Sequence Searching on Multicore

One of the used of string matching is to search DNA sequence in the DNA database. This simple operation can be done in hours or days, because the huge size of DNA sequence database. On the other hand, the potential of multicore for DNA sequence searching is not fully explored due to the difficulty of multicore programming. This paper evaluates several key string matching algorithms using a comprehensive simulation framework. Starting from decoding compressed DNA sequence and instructions processor profiling, the framework constructs task graphs for string matching algorithms. Then task graphs are mapped onto multicore. The mapping technique is based on a random algorithm result in a high mapping quality. The key feature of this paper is that entire processes are automated and it requires users little understanding of the complexity of algorithms and multicore hardware architecture. DNA compressed can save up to 75% space and our framework can be as a guidance to utilize multicore for searching DNA pattern.