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.

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:

• global_alignment.pl

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
• 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