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Parameterized String Matching Algorithms with Application to Molecular Biology

Prasad, R and Agarwal, S and Misra, Sanjay (2010) Parameterized String Matching Algorithms with Application to Molecular Biology. Nigeria Journal of Technological Ressearch, 5.

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In the molecular biology, it is said that two biological sequences tend to have similar properties if they have similar 3-D structures. Hence, it is very important to find not only similar sequences in the string sense, but also structurally similar squences from the database. Parameterized string matchin has been used to find structurally similar sequences from the database. In the parameterized string matching problem, a given pattern P is said to match with a sub-string t of the text T, if there exist a bijection from the symbols of P to the symbols of t. Salmela and Tarhio solve the parameterized string matching problem in sub-linear time by applying the concept of q-gram in the Horspool algorithm (FPBMH). In this paper, we extend the Boyer Moore type algorithms: Smith, Raita and Quick Search, to solve the same problem by using the q-gram. We compare the performance of: FPBMH, Smith, Raita, and Quick search algorithms on DNA alphabet and found that Smith algorithm perform better than FPBMH algorithm.

Item Type: Article
Uncontrolled Keywords: Algorithm, prev-encoding, parameterized matching, molecular biology, and RGF String.
Subjects: Q Science > QA Mathematics
Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Divisions: Faculty of Engineering, Science and Mathematics > School of Electronics and Computer Science
Depositing User: Mrs Patricia Nwokealisi
Date Deposited: 23 Mar 2014 20:12
Last Modified: 23 Mar 2014 20:12

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