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17 Pages, 1,067 KB 
Efficient Alignment of Very Long Sequences
Abstract:
We consider the problem of aligning two very long biological sequences. The score for the best alignment may be found using the Smith-Waterman scoring algorithm while the best alignment itself may be determined using Myers and Miller’s alignment algorithm. Neither of these algorithms takes advantage of computer caches to obtain high efficiency. We propose cache-efficient…
Read More(This article belongs to the SP5 (Special Issue on Multidisciplinary Sciences and Engineering 2018) & Section Interdisciplinary Applications of Computer Science (CSI))