A modified algorithm for species specific motif discovery

Motif discovery can be used to categorize unknown DNA sequences into their corresponding families. For this study, PSO was modified for discovering motif. The modified Linear-PSO is chosen even though it is a slower because linear search is not a choice but a necessary criteria for identifying motif of pig (Sus Scrofa). Pig motif identification is a critical for halal authentication. The modified Linear-PSO algorithm used linear number for population initializing and next position updating. For each cycle, only a particle called ‘target motif’ was selected and compared with other DNA sequences for fitness calculation. Motif discovered can be used as a standard motif for species identification. Experimental results show that the modified algorithm is able to identify motifs as expected. This study showed that a slower algorithm is still needed and has value based on how critical the problem is.