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!