Comparing
two sequences of the same type (e.g.
genomic vs. genomic):
Shows
you how similar sequences are.
Highlight
regions of similarity or difference.
Find
best region of similarity.
Look
for overlaps.
Often
more exacting alignments than database scanning programs.
Comparing
genomic vs. EST or genomic vs. protein:
Reveal
coding regions
Reinforce
gene predictive methods
Many programs have been written to do pairwise comparisons, some of the
major types are discussed below: