ON THE HIGH PERFORMANCE COMPUTING FOR MOTIF DISCOVERY IN DNA SEQUENCES

In bioinformatics, one of the most important research problems is the Motif discovery in DNA sequences. The algorithm having accuracy and speed has always been the goal of research in bioinformatics, for solving this problem. Therefore, the idea of this research study is to modify the random projection algorithm to be implemented using high performance computing technique (i.e., the R package pbdMPI). The steps that are needed to achieve this objective are the main focus of this study, i.e. preprocessing data, splitting data according to number of batches, modifying and implementing random projection in the pbdMPI package, and then aggregating the results. To validate this approach, some experiments have been conducted. Several benchmarking data were used in this study by sensitivity analysis on number of cores and batches. Experimental results show that computational cost can be reduced. Thus, the proposed approach can be used for the motif discovery effectively and efficiently.