A Simple, Fast, Filter-Based Algorithm for Approximate Circular Pattern Matching

• Published in: IEEE transactions on nanobioscience 2016-03, Vol.15 (2), p.93-100
• Main Authors: Azim, Md Aashikur Rahman, Iliopoulos, Costas S., Rahman, M. Sohel, Samiruzzaman, M.
• Format: Magazinearticle
• Language: English
• Subjects: Algorithms; Approximation; Approximation algorithms; Circular DNA sequence; circular pattern matching; Circularity; Computational Biology - methods; Context; DNA; DNA, Circular - analysis; DNA, Circular - chemistry; DNA, Circular - genetics; Hamming distance; Nanobioscience; Nanostructure; Pattern analysis; Pattern matching; pattern recognition; Pattern Recognition, Automated - methods; Sequence Analysis, DNA - methods; State of the art; Texts; Weight reduction
• ISSN: 1536-1241; 1558-2639
• DOI: 10.1109/TNB.2016.2542062

This paper deals with the approximate version of the circular pattern matching (ACPM) problem, which appears as an interesting problem in many biological contexts. The circular pattern matching problem consists in finding all occurrences of the rotations of a pattern P of length m in a text T of length n. In ACPM, we consider occurrences with k-mismatches under the Hamming distance model. In this paper, we present a simple and fast filter-based algorithm to solve the ACPM problem. We compare our algorithm with the state of the art algorithms and the results are found to be excellent. In particular, our algorithm runs almost twice as fast than the state of the art. Much of the efficiency of our algorithm can be attributed to its filters that are effective but extremely simple and lightweight.