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Many modern sequence alignment tools implement fast string matching using thespace efficient data structure called FM-index. The succinct nature of thisdata structure presents unique challenges for the algorithm designers. In thispaper, we explore the opportunities for parallelization of the exact andinexact matches and present an efficient SIMD solution for the Occ portion ofthe algorithm. Our implementation computes all eight Occ values required forthe inexact match algorithm step in a single pass. We showcase the algorithmperformance in a multi-core genome aligner and discuss effects of the memoryprefetch.

Vectorized Character Counting for Faster Pattern Matching