| Parameter |
Sence |
Recommended values |
| Start word length |
Start length of motiff for Multiple sequence alignment.
This value will be reduced on algorithm steps |
10..20 |
| Max N Mismatches |
Number of mismatches allowed for motiff search in Multiple sequence alignment |
about 40% of Start Word length
This value will be reduced on algorithm steps |
| Min score |
Minimal Z-score that wiil be taken into account |
2.0 .. 2.5 |
| Gap parameter |
This parameter defines gap scoring.
the grater this value is the stronger gap will be panalysed |
0.5 .. 1.5 |
| Min information |
Minimum of information content of colomn.
If inforation content of a column is less than given value the column should be not included into alignment.
the grater this value is the stronger gap will be panalysed |
0.5 .. 1.5 |
| Iterations |
Number of iterations for profile refining
|
2 .. 5 |
| Max loop |
Max energy of a helix
|
5 .. 6 |
| Min Energy |
Minimal energy of a helix. Calculated using approximated table:
|
A |
C |
G |
T |
| A |
-8 |
0 |
-8 |
2 |
| C |
0 |
-8 |
3 |
-8 |
| G |
-8 |
3 |
-8 |
1 |
| T |
2 |
-8 |
1 |
-8 |
|
5.0 .. 6.5 |