An efficient solution for aligning huge DNA sequences

Recently, many parallel solutions were proposed in order to accelerate the exact methods for optimal alignment of DNA sequences. However, most of these solutions calculate only the alignment similarity score without finding the actual alignment. This paper presents an efficient solution to find the optimal alignment of the huge DNA sequences. This solution releases the condition of the sequence size to be in megabyte-scale instead of few kilobytes. The fundamental innovation in this work is developing an efficient, linear space complexity, parallel solution to achieve the optimum alignment with relatively good performance. The shared memory parallel architecture is the focus of this work therefore; we have considered off-the-shelf systems like multi-core CPUs as well as advanced shared memory platforms. Experimental results show that the proposed solution achieved high records compared to other solutions that targeted the same goal with less hardware requirements.