This work presents GenDP, a programmable dynamic programming acceleration framework that supports general-purpose acceleration for genomics kernels in commonly used sequencing pipelines.

The edit distance is a fundamental measure of sequence similarity, defined as the minimum number of character insertions, deletions, and substitutions needed to transform one string into the other.

The edit distance problem is widely known, as it is often taught as part of the undergraduate curriculum to illustrate two-dimensional dynamic programming. Theoreticians have studied the problem ...

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For 40 years, computer scientists have tried in vain to find a faster way to do an important calculation known as “edit distance.” Thanks to groundbreaking work from two researchers at MIT ...