This section is all about how sequence comparisons are made. When we look forward to compare two sequences, we are interested in finding significant areas of similarity. The problem is to define what significant means in biological terms. The conclusion is that we can not simply put both sequences one alongside the other, but that we must compare them in all possible shiftings looking for the best alignment. This, however is not the end of the story.
Biological organisms use many mechanisms of change.
Simple conversion from one residue to another is just one of them, but insertions and deletions, although less common, happen quite often too. Looking at only two sequences we have no way of telling whether it is an insertion or a deletion what has happened, hence we call it simply an indel . In our example above we have increased similarity at the start of both sequences at the cost of many gaps, just to add a few more coincidences. Some times it is, and some times it is not. If we need to degrade too much the sequences it probably will not.