End GapsConsider the following alignment:
There are four matches, yielding +4 points, and 10 alignments with gaps, which, given a gap penalty of -2, yields -20 points, for a total score of -16.
Now realign the sequences as follows:
Now we have 5 matches, yielding +5 points, and 8 alignments with gaps, yielding -16 points, for a total of -11 points. This is better?
Well, -11 is a better score than -16 mathematically, but the context of our
comparison is biology.
We're interested in the idea that the similarity of the two sequences may be
due to a series of
changes over time: insertions, deletions, etc. In that light the first sequence
is more interesting
than the second despite its lower score. It is more interesting to view the
string ACCTA as
serving some biological purpose that, in being inserted in the first string
almost intact, improved
that sequence. The letters of a small sequence can always be shuffled about
as was done in the
second alignment, but there's almost no way to determine if that is