An efficient solution for aligning huge DNA sequences

Ahmad M. Hosny, Howida A. Shedeed, Ashraf S. Hussein, Mohamed F. Tolba
2011 The 2011 International Conference on Computer Engineering & Systems  
Recently, many parallel solutions were proposed in order to accelerate the exact methods of aligning huge DNA sequences. However, most of these solutions restrict the sequence's sizes to be in kilobytes, in such a way that megabyte-scale genome comparison cannot be achieved. In addition, 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
more » ... n releases the condition of the sequence size to be in megabyte-scale instead of few kilobytes. The fundamental innovation in this work is developing 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 and therefore we have considered offthe-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.
doi:10.1109/icces.2011.6141059 fatcat:2esc64abqrhuzcneodwrpje2xa