Penalization for GAPS
Sequential (usually protein) alignments can be penalized by the presence
of gaps. A gap is a hole in the sequential correspondence between atoms
of the structures. For example, a structural alignment corresponding to
the following sequence alignment,
| 144 |
GSHMEEMIRSLQQRPEPT---WDLIHIAT |
193 |
| 202 |
EE--LQ--KSIGHKPEPTDEEWELIKTVT |
247 |
contains three gaps. If one thinks that our alignment should be strictly
sequential, it is possible to increase the penalization for gaps. The
scores are designed, on the other side, to automatically use or not gap
penalties. For instance, the Structal score uses a default penalty of
10. per gap, but the TM-Score does not penalize them. The penalization
for gaps can, nevertheless, be adjusted in order to provide different
alignment results which may fit better the expectations of the user.