On Designing Parallel Algorithm for DNA Sequence Homology Search Tool

Abd Rahman, Mohd Nordin (2009) On Designing Parallel Algorithm for DNA Sequence Homology Search Tool. In: UII Conference on Since and Technology, 24-25 January 2009, Jogjakarta.

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Abstract

Developing efficient techniques and procedures to support DNA sequence retrieving is a vital issue in bioinformatics application. The common methods used in this application are dynamic programming and heuristics methods. Dynamic programming method produces an optimal result of DNA comparison. However, it requires longer time and bigger space to complete the process. Heuristics method can speedup the DNA comparison process but will reduce the sensitivity of similarity search result. We have developed a fast-optimal DNA sequence similarity search model known as FRA-Search model. Automaton based exact string matching algorithm is employed to filter irrelevant database sequences from being computed for optimal alignment process. To enhance the process of filtering, the rough sets theory has been employed to classify and reduct the dataset. Finally, the enhanced model is reengineered to run under parallel processing mode. This paper discusses the detailed on designing the parallel FRA-Search algorithm. The performance of parallel computation in FRA-Search model also will be discussed.

Item Type: Conference or Workshop Item (Paper)
Subjects: Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Faculty / Institute: Faculty of Informatics & Computing
Depositing User: Dr Mohd Nordin Abdul Rahman
Date Deposited: 30 Nov 2014 10:10
Last Modified: 01 Dec 2014 02:10
URI: http://erep.unisza.edu.my/id/eprint/1253

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