ABS: Sequence alignment by scanning

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Talal Bonny, et al., "ABS: Sequence alignment by scanning." In 2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2011, 1.

Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called ‘Alignment By Scanning’ (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the ‘FASTA’ (which is heuristic) and the ‘Needleman-Wunsch’ (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences.