Abstract
A program is described for simultaneously aligning two or more molecular sequences which is based on first finding common segments above a specified length and then piecing these together to maximize an alignment scoring function. Optimal as well as near-optimal alignments are found, and there is also provided a means for randomizing the given sequences for testing the statistical significance of an alignment. Alignments may be made in the original alphabets of the sequences or in user-specified alternate ones to take advantage of chemical similarities (such as hydrophobic-hydrophilic).
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Selected References
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