A Coarse-Grained Pipeline Architecture for Sequence Alignment

Abstract

A coarse-grained pipelined engine for DNA sequence alignment technique is exhibited in this manuscript. A pipelined structure with an alignment co-processor are designed for rapid and highly developed DNA sequence alignment. Moreover, this architecture efficiently uses memory windows to store array values, in lieu of using GPU and CAM that use up huge power and cost, to improve the space and speed complexity of sequence alignment in real time. A pipeline scheme has been embedded in the hardware architecture for array formation operations to accomplish temporal parallelism to prepare direction array. For a large amount of sequences, this architecture consumes reasonably low memory space and uses a dedicated alignment co-processor to acquire desired aligned sequences. The entire hardware architecture is tested using a customise unit considering various length of database and query sequences. The numerical results show that the engine takes reasonably less time to align sequences than existing designs. This has been achieved by the proposed one by avoiding comparison operations during sequence alignment phase. It is also observed that the pipeline engine provides reasonably acceptable speed-up (S ∝ N) that depends on the number of nucleotides (N) of database∝ sequences.