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首页> 外文期刊>International Journal of Engineering Research and Applications >A Novel Framework for Short Tandem Repeats (STRs) Using Parallel String Matching
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A Novel Framework for Short Tandem Repeats (STRs) Using Parallel String Matching

机译：一种使用并行字符串匹配的短串联重复序列（STR）的新颖框架

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Short tandem repeats (STRs) have become important molecular markers for a broad range of applications, such as genome mapping and characterization, phenotype mapping, marker assisted selection of crop plants and a range of molecular ecology and diversity studies. These repeated DNA sequences are found in both Plants and bacteria. Most of the computer programs that find STRs failed to report its number of occurrences of the repeated pattern, exact position and it is difficult task to obtain accurate results from the larger datasets. So we need high performance computing models to extract certain repeats. One of the solution is STRs using parallel string matching, it gives number of occurrences with corresponding line number and exact location or position of each STR in the genome of any length. In this, we implemented parallel string matching using JAVA Multithreading with multi core processing, for this we implemented a basic algorithm and made a comparison with previous algorithms like Knuth Morris Pratt, Boyer Moore and Brute force string matching algorithms and from the results our new basic algorithm gives better results than the previous algorithms. We apply this algorithm in parallel string matching using multi-threading concept to reduce the time by running on multicore processors. From the test results it is shown that the multicore processing is a remarkably efficient and powerful compared to lower versions and finally this proposed STR using parallel string matching algorithm is better than the sequential approaches.
机译：短串联重复序列（STR）已成为广泛应用的重要分子标记，例如基因组图谱和表征，表型作图，农作物标记辅助选择以及一系列分子生态学和多样性研究。在植物和细菌中都发现了这些重复的DNA序列。找到STR的大多数计算机程序都无法报告其重复模式的出现次数，准确的位置，并且很难从较大的数据集中获得准确的结果。因此，我们需要高性能的计算模型来提取某些重复项。一种解决方案是使用并行字符串匹配的STR，它给出出现的次数和相应的行号，以及每个STR在任何长度的基因组中的确切位置或位置。在此，我们使用具有多核处理功能的JAVA多线程技术实现了并行字符串匹配，为此，我们实现了一种基本算法，并与以前的算法（例如Knuth Morris Pratt，Boyer Moore和Brute force字符串匹配算法）进行了比较，并从结果中得出了新的基础该算法比以前的算法提供了更好的结果。我们将此算法应用于使用多线程概念的并行字符串匹配中，以通过在多核处理器上运行来减少时间。从测试结果可以看出，与较低版本相比，多核处理具有显着的效率和功能，并且最终提出的使用并行字符串匹配算法的STR比顺序方法更好。

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