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Table 6 The performance of w-SSHash on the permuted string collections Cod, Kestrel, Human, and Bacterial

From: On weighted k-mer dictionaries

Dataset

\(H_0(W)\)

bpk

 

GB

qtm

Cod

0.441

6.98 + 0.19

(\(2.35\times \))

0.45

1.3

Kestrel

0.089

6.49 + 0.02

(\(3.80\times \))

0.94

1.1

Human

0.453

8.28 + 0.22

(\(2.06\times \))

2.66

1.7

Bacterial

1.890

8.22 + 0.24

(\(7.81\times \))

5.66

1.7

  1. We report the empirical entropy of the weights (\(H_0(W)\)), the dictionary space in average bits/\(k\)-mer (bpk) and total GB, and query-time in average μs/\(k\)-mer (qtm). The space is indicated as \(x+y\), where x is the space of SSHash (without the weights) and y is the space for the encoding of the weights. In parentheses we report the space reduction of the encoded weights compared to the empirical entropy of the weights
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Algorithms for Molecular Biology

ISSN: 1748-7188