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
Multiple sequences alignment:
To highlight regions of
similarity, divergence and mutations.
To elicit more information
than from a single sequence.
(e.g. for creating a
profile to find other more distant family members.)
To reveal errors in protein
sequence prediction.
To improve secondary
structure and other predictions.
For evolutionary analysis
(phylogeny).
For finding novel
motifs.
For selection of
appropriate primers for a gene family.