Lecture GK-3

Pairwise sequence alignment

Aims

• To introduce the basic principles of pairwise sequence alignment.
• To introduce methods for assessing the significance of sequence alignment scores.

Objectives

After this lecture you will be able to:

• describe and compute of simple measures of sequence similarity;
• describe the relationship between dotplots and sequence alignments;
• implement and apply a dynamic programming algorithm to find an optimal pairwise sequence alignment;
• describe the difference between global and local alignment algorithms;
• describe how z-scores are used in assessing the significance of global alignment scores;
• describe how the values in substitution matrices reflect similarities and differences in the properties of amino acid residues, and also reflect the relative abundances of different amino acid residues;
• be aware of which substitution matrices are suitable for different tasks.

Supplementary Material

The lecture handout, featuring some of the lecture slides, is available on-line (one per page, four per page).

Web-based programs illustrating topics from the lecture:

• Dotplot
• Global Alignment
• Local Alignment

The global alignment program described in the lecture (local access only):

• global_alignment.pl