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Table 2 Performances of four programs on searching all 1458 D. sp. CBDB1 protein sequences against DS1

From: GRASPx: efficient homolog-search of short peptide metagenome database through simultaneous alignment and assembly

Pathway BLASTP PSI-BLAST FASTM GRASPx
C4 M5 R6 C M R C M R C M R
TCA cycle1 0.61 0.38 0.37 0.69 0.44 0.42 0.57 0.32 0.28 0.88 0.64 0.59
2 0.66 0.44 0.42 0.75 0.55 0.52 0.44 0.10 0.08 0.88 0.74 0.69
Pentose 0.67 0.71 0.64 0.76 0.76 0.68 0.54 0.52 0.40 0.85 0.78 0.64
phosphate 0.61 0.62 0.50 0.71 0.72 0.61 0.41 0.41 0.26 0.87 0.84 0.74
Fructose 0.61 0.48 0.38 0.53 0.52 0.42 0.38 0.38 0.26 0.75 0.66 0.53
mannose 0.50 0.51 0.38 0.56 0.58 0.45 0.38 0.38 0.22 0.80 0.75 0.64
Pyruvate 0.55 0.41 0.40 0.64 0.48 0.45 0.42 0.25 0.22 0.72 0.56 0.52
  0.59 0.43 0.40 0.69 0.56 0.53 0.32 0.08 0.07 0.78 0.66 0.63
Methane 0.57 0.38 0.27 0.63 0.43 0.31 0.56 0.31 0.21 0.75 0.56 0.44
  0.66 0.49 0.35 0.70 0.56 0.42 0.57 0.28 0.12 0.82 0.67 0.53
Nitrogen 0.54 0.53 0.51 0.56 0.55 0.54 0.05 0.05 0.05 0.59 0.59 0.58
  0.35 0.34 0.34 0.53 0.52 0.51 0.01 0.01 0.01 0.69 0.69 0.68
Sulfur 0.79 0.72 0.68 0.83 0.75 0.70 0.56 0.48 0.38 0.84 0.75 0.68
  0.75 0.65 0.57 0.80 0.71 0.64 0.22 0.15 0.12 0.86 0.78 0.73
Overall3 0.59 0.51 0.30 0.66 0.57 0.36 0.52 0.43 0.22 0.71 0.64 0.44
  0.65 0.59 0.40 0.72 0.65 0.47 0.59 0.49 0.23 0.77 0.72 0.55
  1. 1: The first row indicates the area under curves (AUC) for the corresponding programs. 2: The second row indicates the F-scores for the corresponding programs. 3: The overall performance is calculated on all 1458 protein sequences annotated in the D. sp. CBDB1 genome. 4: ‘C’ indicates close homologs (defined by TBLASTN E-value cutoff 10-10). 5: ‘M’ indicates moderate homologs (defined by TBLASTN E-value cutoff 10-3). 6: ‘R’ indicates remote homologs (defined by TBLASTN E-value cutoff 10). The highest performances among all programs are bolded