BackgroundThe number of k-words shared between two sequences is a simple and effcient alignment-free sequence comparison method. This statistic, D2, has been used for the clustering of EST sequences. Sequence comparison based on D2 is extremely fast, its runtime is proportional to the size of the sequences under scrutiny, whereas alignment-based comparisons have a worst-case run time proportional to the square of the size. Recent studies have tackled the rigorous study of the statistical distribution of D2, and asymptotic regimes have been derived. The distribution of approximate k-word matches has also been studied.
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