• Structures: VAST, Cn3D, and de novo prediction NHGRI Current Topics in Genome Analysis 2005 Biological Sequence Analysis I

Why do sequence alignments? • Provide a measure of relatedness between nucleotide or amino acid sequences • Determining relatedness allows one to draw biological inferences regarding • structural relationships • functional relationships • evolutionary relationships importance of using correct terminology Defining the Terms • The quantitative measure: Similarity • Always based on an observable • Usually expressed as percent identity • Quantify changes that occur as two sequences diverge • substitutions • insertions • deletions • Identify residues crucial for maintaining a protein’s structure or function • High degrees of sequence similarity might imply • a common evolutionary history • possible commonality in biological functio