Lecture GK-1

Pairwise sequence alignment

Aims

• To introduce the basic principles of pairwise sequence alignment.

Objectives

After this lecture you will:

• be aware of simple measures of sequence similarity;
• understand the relationship between dotplots and sequence alignments;
• understand how a dynamic programming algorithm finds an optimal pairwise sequence alignment;
• understand the difference between global and local alignment algorithms.

Supplementary Material

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

Web-based programs illustrating topics from the lecture:

• Dotplot
• Global Alignment
• Local Alignment

Programs described in the lecture (local access only):

• dotplot.c
• Dotplot.java
• global_alignment.c
• GlobalAlignment.java