Lecture 2

Pairwise sequence alignment

Aims

• To introduce the basic principles of pairwise sequence alignment.
• To describe heuristic methods for finding local alignments.

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 the BLAST and FASTA programs find local alignments when searching for matches in large databases.

Supplementary Material

Some of the lecture slides are available on-line (1 per page, 4 per page).

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,
• 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
• Altschul, S.F., Gish, W., Miller, W., Myres, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
  doi:10.1016/S0022-2836(05)80360-2
• Pearson, W.R. and Lipman, D.J. (1988) Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences, 85, 2444-2448.
  doi:10.1073/pnas.85.8.2444