Table 2 |
||||||
|
Parameterization of negative transition scores from gap penalties. |
||||||
|
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 |
|
|
||||||
|
α and β are replaced with α' and β' for the specific cases described in the text. The IR_cl to IL_cl transition is never allowed in these models. |
||||||
|
Klein and Eddy BMC Bioinformatics 2003 4:44 doi:10.1186/1471-2105-4-44 |
||||||
