Lecture 2

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

Some of the lecture slides are available on-line (PDF).

Web-based programs illustrating topics from the lecture:

• Dotplot
• Global Alignment
• Local Alignment

References

• Needleman, S.B. and Wunsch, C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
  doi:10.1016/0022-2836(70)90057-4, PubMed
• Smith, T.F. and Waterman, M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
  doi:10.1016/0022-2836(81)90087-5, PubMed