PROTEIN PARAMETERS

Matrix
- BLOSUM62
- BLOSUM50
- PAM120
- PAM250
See the survey of David Wheeler to know more about matrices.
Gaps
- Cut Gap: gap penalty for the first residue.
- Ext Gap: gap penalty for the next residues.
See the reference below to understand the way gaps are handled:
```
Gotog, O. (1982). An Improved Algorithm for Matching 
Biological Sequences.J. Mol. Biol. 162, 705-708.
```
Alignements
- Number of alignments to be shown.
- dIsplay from highest to lowest score.