A scalable high-throughput pipeline architecture for DNA sequence alignment

A novel scalable architecture for DNA sequence alignment has been presented in this paper. A pipelined architecture with a dedicated backtrack processor have been designed for fast and sophisticated DNA sequence alignment. Additionally, instead of using CAM which consumes huge power, this architecture efficiently uses RAM to boost the speed of DNA sequence alignment in real time. This architecture incorporates a pipeline structure for matrix fill operation to achieve temporal parallelism in preparing substitution matrix for a number of sequences and a backtrack processor to obtain aligned sequences. Besides, this paper presents a comparative analysis on the processing time of this architecture using three numerous cases based on temporal and special parallelism, namely, dedicated, moderately-dedicated and shared logic components. The complete architecture has been simulated for 1000 database sequences considering both 16 and 32 nucleotides as DNA sequence size.