Pattern Matching for DNA Sequencing Data Using Multiple Bloom Filters

Najam, Maleeha and Rasool, Raihan Ur and Ahmad, Hafiz Farooq and Ashraf, Usman and Malik, Asad Waqar (2019) Pattern Matching for DNA Sequencing Data Using Multiple Bloom Filters. BioMed Research International, 2019. pp. 1-9. ISSN 2314-6133, DOI

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Storing and processing of large DNA sequences has always been a major problem due to increasing volume of DNA sequence data. However, a number of solutions have been proposed but they require significant computation and memory. Therefore, an efficient storage and pattern matching solution is required for DNA sequencing data. Bloom filters (BFs) represent an efficient data structure, which is mostly used in the domain of bioinformatics for classification of DNA sequences. In this paper, we explore more dimensions where BFs can be used other than classification. A proposed solution is based on Multiple Bloom Filters (MBFs) that finds all the locations and number of repetitions of the specified pattern inside a DNA sequence. Both of these factors are extremely important in determining the type and intensity of any disease. This paper serves as a first effort towards optimizing the search for location and frequency of substrings in DNA sequences using MBFs. We expect that further optimizations in the proposed solution can bring remarkable results as this paper presents a proof of concept implementation for a given set of data using proposed MBFs technique. Performance evaluation shows improved accuracy and time efficiency of the proposed approach. © 2019 Maleeha Najam et al.

Item Type: Article
Uncontrolled Keywords: Data structures; Algorithms; Suffix arrays
Subjects: Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Divisions: Faculty of Computer Science & Information Technology
Depositing User: Ms. Juhaida Abd Rahim
Date Deposited: 28 Feb 2020 01:38
Last Modified: 28 Feb 2020 01:38

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