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Table 2 Number and percentage of clusters in the different evaluation groups for proteinortho and porthoDom

From: Domain similarity based orthology detection

Method

Proteinortho

PorthoDom

PorthoDom

PorthoDom

PorthoDom

  

(O1, norepeat)

(O1, repeat)

(O2, norepeat)

(O2, repeat)

Superset (%)

5442 (26.13)

5311 (28.53)

5274 (28.26)

5172 (27.58)

5161 (27.4)

Subset (%)

2639 (12.67)

2054 (11.03)

2077 (11.13)

2104 (11.22)

2171 (11.52)

Identical (%)

1945 (9.34)

1311 (7.04)

1333 (7.14)

1351 (7.21)

1328 (7.05)

New (%)

7419 (35.62)

7396 (39.73)

7445 (39.89)

7580 (40.43)

7622 (40.45)

Absent (%)

3383 (16.24)

2545 (13.67)

2536 (13.59)

2543 (13.56)

2559 (13.58)

  1. The domain content similarity cut-off of porthoDom was set to 0.5 and different combination of parameters affecting order (O1, O2) and repeats (with or without) were tested.