Lecture GK-1

Pairwise sequence alignment

Aims

• To introduce the basic principles of pairwise sequence alignment.

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.

Supplementary Material

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