A Fast Hybrid Algorithm Approach for the Exact String Matching Problem Via Berry Ravindran and Alpha Skip Search Algorithms

Abstract

<b>Problem statement:</b> String matching algorithm had been an essential means for searching&#13; biological sequence database. With the constant expansion in scientific data such as DNA and Protein;&#13; the development of enhanced algorithms have even become more critical as the major concern had&#13; always been how to raise the performances of these search algorithms to meet challenges of scientific&#13; information. <b>Approach:</b> Therefore a new hybrid algorithm comprising Berry Ravindran (BR) and&#13; Alpha Skip Search (ASS) is presented. The concept is based on BR shift function and combines with&#13; ASS to ensure improved performance. <b>Results:</b> The results obtained in percentages from the proposed&#13; hybrid algorithm displayed superior results in terms of number of attempts and number of character&#13; comparisons than the original algorithms when various types of data namely DNA, Protein and English&#13; text are applied to appraise the hybrid performances. The enhancement of the proposed hybrid&#13; algorithm performs better at 71%, 60% and 63% when compared to Berry-Ravindran in DNA, Protein&#13; and English text correspondingly. Moreover the rate of enhancement over Alpha Skip Search&#13; algorithm in DNA, Protein and English text are 48%, 28% and 36% respectively. <b>Conclusion:</b> The&#13; new proposed hybrid algorithm is relevant for searching biological science sequence database and also&#13; other string search systems

Parallel DNA Sequence Approximate Matching with Multi-Length Sequence Aware Approach

“…Searching of exact or approximate pattern match is one of the fundamental problems in computer science. Many algorithms have been developed in the last three decades, focusing on the general problem [6] [10]. Also, the recent advances in genomics research, the speed of processor development growth, and the increased amount of data have been open the challenge in this era.…”

“…Also, the recent advances in genomics research, the speed of processor development growth, and the increased amount of data have been open the challenge in this era. [6] Proposed a new hybrid algorithm for string matching (ASSBR) that compromises of Berry Ravindran (BR) shift function and Alpha Skip Search (ASS) algorithm to improve the performance. The hybrid algorithm tested by three types of data: DNA, Protein, and English text; and showed a better performance than both original algorithms in terms of number of attempts and character comparisons.…”

Fast Hybrid String Matching Algorithm based on the Quick-Skip and Tuned Boyer-Moore Algorithms

“…Berry Ravindran-Skip Search (BRSS) Algorithm Berry Ravindran-Skip Search (BRSS) algorithm [11] is a combination of Berry Ravindran and Skip Search (SS) algorithms. The preprocessing phase consists of building the bucket list for the SS algorithm and the (brBc) table.…”