Predefined limits
Many decisions in HIVIntact logic rely on predefined “limits”. This page lists all of them, except for the standard constants such as the 5% limit for p-value.
ORF lengths
| ORF name | deletion tolerance | insertion tolerance |
|---|---|---|
| gag | -30 | +90 |
| pol | -30 | +90 |
| env | -100 | +300 |
| vif | -30 | +90 |
| vpr | -30 | +90 |
| tat_exon1 | -30 | +90 |
| rev_exon1 | -30 | +90 |
| vpu | -30 | +90 |
| tat_exon2 | -30 | +90 |
| rev_exon2 | -30 | +90 |
| nef | -30 | +90 |
Other
The PSI error tolerance is 10.
The RRE error tolerance is 20.
Minimum tolerable sequence length is 8000.
Maximum tolerable number of nucleotides impacted by frame shifts is 10% of the ORF’s length.