A High-Performance DNA Multiple Pattern Matching Algorithm Based on Index Binding and ASCII Hashing
kaisar, M., Hanafy, I., El-Attar, N., Awad, W. (2025). A High-Performance DNA Multiple Pattern Matching Algorithm Based on Index Binding and ASCII Hashing. EKB Journal Management System, 2(1), 9-16. doi: 10.21608/jaiep.2025.395293.1016
monica kaisar; Ibrahim Hanafy; Noha El-Attar; Wael Awad. "A High-Performance DNA Multiple Pattern Matching Algorithm Based on Index Binding and ASCII Hashing". EKB Journal Management System, 2, 1, 2025, 9-16. doi: 10.21608/jaiep.2025.395293.1016
kaisar, M., Hanafy, I., El-Attar, N., Awad, W. (2025). 'A High-Performance DNA Multiple Pattern Matching Algorithm Based on Index Binding and ASCII Hashing', EKB Journal Management System, 2(1), pp. 9-16. doi: 10.21608/jaiep.2025.395293.1016
kaisar, M., Hanafy, I., El-Attar, N., Awad, W. A High-Performance DNA Multiple Pattern Matching Algorithm Based on Index Binding and ASCII Hashing. EKB Journal Management System, 2025; 2(1): 9-16. doi: 10.21608/jaiep.2025.395293.1016

A High-Performance DNA Multiple Pattern Matching Algorithm Based on Index Binding and ASCII Hashing

Journal of Artificial Intelligence in Engineering Practice
Volume 2, Issue 1, April 2025, Page 9-16  XML PDF (529.88 K)
Document Type: Original Article
DOI: 10.21608/jaiep.2025.395293.1016
View on SCiNiTO View on SCiNiTO
Authors
monica kaisar email 1; Ibrahim Hanafy2; Noha El-Attar3; Wael Awad4
1Institute of Management Information Systems, Suez 14028, Egypt
2Department of Mathematics and Computer Science, Faculty of Science, Port Said University, Port Said 42521, Egypt
3Faculty of Computers and Artificial Intelligence, Benha University, Benha 13511, Egypt
4Faculty of Computers and Artificial Intelligence, Damietta University, 34511 Damietta, Egypt
Abstract
Beyond health, the exponential trend in the volume of genomic data, combined with broad access to personal genome sequencing, has generated a pressing demand for fast and  scalable algorithms to explore patterns in DNA sequences. Rapid and specific identification of DNA sub-sequences is of critical importance in various applications,  such as personalized medicine, evolutionary biology, and forensic sciences. A new algorithm for exact multiple pattern matching in DNA sequences is presented in this paper. The approach is based on combining an index binding technique with a fast and lightweight hashing method that utilizes ASCII encoding. The method builds an  index table for each test pattern nucleotide and computes an integer hash value using the ASCII values of the test pattern characters. This system of dual filter s is three to four orders of magnitude more efficient than comparing them all. Experimental evaluations using real genomic data demonstrate that the proposed algorithm achieves improved performance compared to established algorithms such as KMP, Boyer-Moore, and Rabin-Karp, particularly in terms of execution time and comparison complexity. The proposed algorithm maintains a time complexity of O(N⋅M) in the worst case, with reduced overhead in typical usage scenarios, making it a practical solution for large-scale DNA sequence analysis.
Keywords
DNA sequence matching; multiple pattern matching; index binding; ASCII hashing; algorithm optimization
Statistics
Article View: 80
PDF Download: 36