Abstract
This unit is presented as a guide to addressing the issue of what to do with a protein sequence once it is obtained. A theoretical background for protein sequence analysis is provided first, followed by a discussion of matrix methods for sequence comparison (Matrix Methods for Sequence Comparison: Dot Plots). Sequence similarity searching is then presented, including the BLAST and FASTA databases. Other aspects of protein sequence analysis covered here are alignment methods, scoring matrices, multiple alignments, cluster methods and trees, and identification of functional sites.
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