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: