Sequence Alignment and Similarity Search:
One goal of sequence alignment is
to enable the researcher to determine whether two sequences display sufficient
similarity to justify the inference of homology. Similarity is an observable
quantity that might be expressed as, say, percent identity or some other
suitable measure. Homology, on the other hand, refers to a conclusion drawn
from these data that two genes share a common evolutionary history. While it
is presumed that homologous sequences have diverged from a common ancestral
sequence through iterative changes, we do not actually know what the ancestral
sequence was (barring the possibility that DNA could be recovered from a
fossil); all we have to observe are the sequences from extant organisms. In a
residue-by-residue alignment it is often apparent that certain regions of a
protein, or perhaps specific amino acids, are more highly conserved than
others. This information may be suggestive of which residues are most crucial
for a maintaining a protein’s structure or function.