A Novel Framework for Short Tandem Repeats (STRs) Using Parallel String Matching

Short tandem repeats (STRs) have become important molecular markers for a broad range of applications, such\ud as genome mapping and characterization, phenotype mapping, marker assisted selection of crop plants and a\ud range of molecular ecology and diversity studies. These repeated DNA sequences are found in both Plants and\ud bacteria. Most of the computer programs that find STRs failed to report its number of occurrences of the\ud repeated pattern, exact position and it is difficult task to obtain accurate results from the larger datasets. So we\ud need high performance computing models to extract certain repeats. One of the solution is STRs using parallel\ud string matching, it gives number of occurrences with corresponding line number and exact location or position\ud of each STR in the genome of any length. In this, we implemented parallel string matching using JAVA Multithreading\ud with multi core processing, for this we implemented a basic algorithm and made a comparison with\ud previous algorithms like Knuth Morris Pratt, Boyer Moore and Brute force string matching algorithms and from\ud the results our new basic algorithm gives better results than the previous algorithms. We apply this algorithm in\ud parallel string matching using multi-threading concept to reduce the time by running on multicore processors.\ud From the test results it is shown that the multicore processing is a remarkably efficient and powerful compared\ud to lower versions and finally this proposed STR using parallel string matching algorithm is better than the\ud sequential approaches