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Table 2 Unsupervised reference algorithms and parameter values proposed in [36]

From: Surveying alignment-free features for Ortholog detection in related yeast proteomes by using supervised big data classifiers

Algorithms

Parameter values

Reciprocal Best Hits (RBH)a

Filter: soft

Alignment: Smith Waterman

E-value: 1e-06

Reciprocal Smallest Distance (RSD)b

E-value thresholds: 1e-05, 1e-10 and 1e-20

Divergence thresholds α: 0.8, 0.5 and 0.2

Orthologous MAtrix (OMA)c

Default parameter values

  1. aMatlab script and BLAST program available in http://www.ncbi.nlm.nih.gov/BLAST/
  2. bPhyton script available in https://pypi.python.org/pypi/reciprocal_smallest_distance/1.1.4/
  3. cStand-alone version available in http://omabrowser.org/standalone/OMA.0.99z.3.tgz
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BMC Bioinformatics

ISSN: 1471-2105

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