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Table 2 Space for the weights in SSHash reported in bits/\(k\)-mer, before and after the run-reduction optimization

From: On weighted k-mer dictionaries

Dataset

\(H_0(W)\)

Before

After

E-Coli

0.206

0.017

(\(12.35\times \))

0.014

(\(15.10\times \))

S-Enterica-100

4.155

0.464

(\(8.96\times \))

0.328

(\(12.66\times \))

Human-Chr-13

0.160

0.135

(\(1.18\times \))

0.108

(\(1.50\times \))

C-Elegans

0.223

0.069

(\(3.23\times \))

0.055

(\(4.05\times \))

  1. For reference, we also report how many times the achieved space is better than the empirical entropy of the weights \(H_0(W)\)
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Algorithms for Molecular Biology

ISSN: 1748-7188