Lecture 2

Aims

• To introduce methods for assessing the significance of sequence alignment scores.
• To introduce PAM and BLOSUM substitution matrices.
• To describe heuristic methods for finding local alignments.
• To introduce HSSP-curves and multiple alignments.

Objectives

After this lecture you will:

• understand how z-scores are used in assessing the significance of global pairwise alignment scores;
• understand why substitution matrices and non-linear gap penalties can produce better alignments;
• be aware of heuristic programs that can find local alignments when searching for matches in large databases;
• understand how structural and functional clues can be inferred from multiple alignments;
• understand how sequence identity and structure similarity are related.

Supplementary Material

The lecture handout, featuring some of the lecture slides, is available on-line.
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