A Parallel ClustalW Algorithm on Multi-Raspberry Pis for Multiple Sequence Alignment

Along with the development of technology in the field of bioinformatics, the cost of DNA sequencing from year to year is getting cheaper. This causes the growth of the genetic database to rise beyond Moore's Law. The rapid growth of genetic databases is one of the main obstacles in conducting sequence alignment. Multiple sequence alignment (MSA) is one important method in analyzing DNA or protein. One of the popular MSA methods among practitioners is Clustal. In sequential programming to process large data, it certainly takes a long time. In addition, sequential programming has limited memory, so it can cause the stack in the program. One way to speed up processing performance is to use parallel programming. MPI is one of the popular parallel computing technologies. In this study, a parallel process was run on a cluster consisting of four Raspberry Pi computers. The experiment used sequence data from BAliBase version 3. From the results of the research, it was shown that at the distance matrix calculation stage it could reach 12.7 times, while at the progressive alignment stage it could reach 5.71 times faster than the sequential process.