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Table 3 Comparison of YASS [27] and geometric hashing using the two-step approach (“Two-step geometric hashing” section) on the same dataset as used in Fig. 3. Sensitivity is the fraction of human conding exons covered by an alignment for YASS or by a seed for geometric hashing

From: Global, highly specific and fast filtering of alignment seeds

Method

Sensitivity

FP

Runtime (min)

Memory

YASS

0.9931

7

107

590 MB

Geometric hashing

0.9979

0

49

28 GB

  1. FP denotes the number of alignments between randomly generated sequences in YASS and the number of such seeds for geometric hashing