PERFORMANCE EVALUATION OF DNA PATTERN MATCHING ALGORITHMS

• Published in: Pakistan journal of science Vol. 74; no. 3; p. 169
• Main Authors: Aziz, I, Shoaib, S, Khurshid, K S, Ahmad, T, Awais, M
• Format: Journal Article
• Language: English
• Published: Lahore Knowledge Bylanes 30.09.2022; Pakistan Association for the Advancement of Science
• Subjects: Algorithms; Analysis; Bioinformatics; Complexity; Computer applications; Data compression; Deoxyribonucleic acid; DNA; Gene sequencing; Literature reviews; Machine learning; Mathematical models; Mutation; Nucleotide sequence; Pattern matching; Performance evaluation; Search methods; Sequence analysis; String matching; Taxonomy
• ISSN: 0030-9877; 2411-0930

Bioinformatics is a new area of research in which DNA, RNA and proteins sequences are dealt. To store, retrieve, analyze, match, align, search, and process these sequences different techniques are existed. Currently a lot of advancements in sequence analysis cause the drastic increase in the DNA database sizes that require more efficient approaches encompass accuracy. Search and analysis of DNA patterns can be performed by using various pattern matching algorithms in the computational biology. The aim of present study is to present taxonomy and performance evaluation of these pattern matching algorithms. The objective of this SLR is to set a research trend and to find a mathematical model to estimate execution search time before scanning whole DNA sequence by following a search strategy. INDEX TERMS: DNA, DNA pattern matching, DNA string matching, DNA pattern matching algorithm, time complexity, and space complexity.