A new approach in pattern matching: Codon Detection in DNA and RNA using hash function (CDDRHF)

Abstract

Detection of different known patterns in any newly found sequence is one of the most important works in the field of Bioinformatics. Given a specific pattern, a long string has to be searched for finding that pattern. That means pattern matching is used for checking the sequence of tokens and the match has to be exact, obviously. These patterns usually have the form of either sequences or tree structures. In DNA and RNA sequences, this type of pattern searching is often needed to detect codons (both met and stop sequences) in it. This paper presents the concept and implementation of a new algorithm codon detection in DNA and RNA using hash function (CDDRHF) for detection of codons in long DNA and RNA sequences, using the concepts of hash function along with metaheuristic approaches. Then the gene between met and stop codons will easily be extracted to be used for proper alignment. This new algorithm works so fast that any DNA or RNA sequence of any length can be used to perfectly search for codons withinseconds.