Table 2 Parameterization of negative transition scores from gap penalties.
From: RSEARCH: Finding homologs of single structured RNA sequences
| Â | To class | |||||
|---|---|---|---|---|---|---|
From class | M_cl | IL_cl | DL_cl | IR_cl | DR_cl | DB_cl |
M_cl | 0 | 1/2α | 1/2α | 1/2α | 1/2α | α |
IL_cl | β + 1/2α | β | β + α | β + α | β + α | β + 3/2α |
DL_cl | β + 1/2α | β + α | β | β + α | β + α | β + 1/2α |
IR_cl | β + 1/2α | N.A. | β + α | β | β + α | β + 3/2α |
DR_cl | β + 1/2α | β + α | β + α | β + α | β | β + 3/2α |
DB_cl | 2β + α | 2β + 3/2α | 2β + 1/2α | 2β + 3/2α | 2β + 1/2α | 2β |