Parallel Computing Technique of Pairwise Alignment by a Dataflow Loop-Structured-Computer

摘要

The pairwise sequence alignment by dynamic programming algorithm is performed in the Loop-Structured-Computer (LSC). The Processing Elements (PEs) of the LSC are connected with each other to make a loop configuration and the number of connected PEs can be varied. However, there is a drawback in using the LSC, i.e., it requires a lot of programming efforts to write the source code. To deal with this, we wrote a program that automatically generates the appropriate LSC source code with the option to vary the initial parameters: amino acid sequences lengths, gap cost, and match/mismatch weights. Pairwise alignment by the dataflow LSC is implemented successfully as confirmed by the correct alignment obtained. We also show in this paper the performance of the LSC in parallel processing involving different number of PEs.