Computational methods in bioinformatics (2013-2014)
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:
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
Last Modified: 31 October 2013
by Graham Kemp