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The Smith-Waterman (SW) algorithm is a local sequence alignment algorithm that attempts to align two biological sequences of varying length such that the alignment score is maximum. In this paper, we propose a new approach to reduce the time needed to perform the SW algorithm. This is done by applying the concept of recursive variable expansion, which exposes more parallelism in the algorithm than...
Sequence alignment is one of the most important activities in bioinformatics. With the ever increasing volume of data in bioinformatics databases, the time for comparing a query sequence with the available databases is always increasing. Many algorithms have been proposed to perform and accelerate sequence alignment activities. This paper introduces a taxonomy of the various sequence alignment algorithms...
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