Linear-PSO with binary search algorithm for DNA Motif Discovery / Hazaruddin Harun

Motif Discovery (MD) is the process of identifying meaningful patterns in DNA, RNA, or protein sequences. In the field of bioinformatics, a pattern is also known as a motif. Numerous algorithms had been developed for MD, but most of these were not designed to discover species specific motifs used in identifying a specifically selected species where the exact location of these motifs also needs to be identified. Evaluation of these algorithms showed that the results are unsatisfactory due to the lower validity and accuracy of these algorithms. At present, DNA sequencing analysis is the most utilised technique for species identification where patterns of DNA sequences are determined by comparing the sequence to comprehensive databases. However, several false and gap sequences had been identified to be present in these databases which lead to false identification. Therefore, this study addresses these problems by introducing a hybrid algorithm for MD. In this study, the MD is a process to discover all possible motifs that existed in DNA sequences whereas Motif Identification (MI) is a process to identify the correct motif that can represent a selected species. Particle Swarm Optimisation (PSO) was selected as the base algorithm that needs improvement and integration with other techniques. The Linear-PSO algorithm was the first version of improvement…