Table 1.
Classification of sequence-to-domain alignment HMMER2 and HMMER3 hits
| Version | Classification | Original E-value | Fold-critical E-value | Remnant E-value |
|---|---|---|---|---|
| HMMER2 | TP (True-positive) | ≤0.1 | ≤10−3.45 | - |
| FP (False-positive) | ≤0.1 | >10−3.45 | ≤10−3.45 | |
| TN (True-negative) | >0.1 | >10−3.45 | - | |
| FN (False-negative) | >0.1 | ≤10−3.45 | - | |
| HMMER3 | TP (True-positive) | ≤10−3 | ≤10−6 | - |
| FP (False-positive) | ≤10−3 | >10−6 | ≤10−6 | |
| TN (True-negative) | >10−3 | >10−6 | - | |
| FN (False-negative) | >10−3 | ≤10−6 | - |
The original E-value of hit is set at 0.1 as recommended by the HMMER2 manual [32] which gives a false-positive rate of 0.53. Using the latter as reference, the equivalent original E-value for HMMER3 is set at 10−3 (false-positive rate of 0.55). For the fold-critical E-value, the false-positive rate is preset at 0.1. These corresponds to the values of 10–3.45 and 10–6, respectively. ‘-’ denotes “don’t care” condition