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Smith-Waterman Algorithm

	1. Assigns a score to each pair of bases    - Uses similarity scores only    - Uses positive scores for related residues    - Uses negative scores for substitutions and gaps
	2. Initializes edges of the matrix with zeros
	3. As the scores are summed in the matrix, any score below 0 is recorded as 0.
	4. Begins the trace back at the maximum value found anywhere in the matrix
	5. Continues until the score falls to 0.

Example:

Scoring metrics are of two types:

Distance (cost) Scores

	The distance between identical residues must be 0.
	The distance, or cost, for aligning two non-identical residues must be greater than 0 (i.e. negative distances are not allowed).

Similarity Scores

	Identical or similar residues have positive scores
	Dissimilar residues can have 0 or even negative scores

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