Graham Kemp's classes
Lecture: Sequence Alignment 1
To introduce methods for assessing the significance of sequence
To describe heuristic methods for finding local alignments.
To explain how PAM and BLOSUM substitution matrices are derived.
After this lecture you will:
understand how z-scores are used in assessing the significance of
global alignment scores;
understand how the BLAST and FASTA programs find local alignments when
searching for matches in large databases;
be aware of e-values and p-values as indicators of the significance
of BLAST hits;
understand how PAM and BLOSUM substitution matrices are derived;
be aware of which substitution matrices are suitable for different tasks.
The lecture handout, featuring some of the lecture slides, is
Statistics of Sequence Similarity Scores by Stephen Altschul, author
The method for deriving BLOSUM matrices is described in:
Henikoff, S. and Henikoff, J.G. (1992)
Amino acid substitution matrices from protein blocks.
Proc Natl Acad Sci USA, 89, 10915-10919
There is an overview of BLAST and substitution matrices in:
Pertsemlidis, A. and Fondon, J.W. (2001)
Having a BLAST
with bioinformatics (and avoiding BLASTphemy),
Genome Biol., 2, reviews2002.1-reviews2002.10.
Last Modified: 11 November 2010
by Graham Kemp