There are three variations
on the theme of sequence comparison.
The BEST region of similarity
between two sequences,
The best OVERALL alignment of two
sequences, or
ALL
regions of similarity between them.
bestfit –
finds
the best single region of similarity & displays it.
gap –
aligns
two sequences over their entire length & displays it.
compare -
finds all regions of potential homology & displays them.
NB: Be
careful when using these programes; it is possible to align one sequence with any other,
if you really want to. False alignments, and the research you plan using
them, may have no biological significance!