TMS145
(2014/2015)
|
Graham Kemp's classes
Lecture 2
Aims
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To introduce a method for assessing the significance of sequence
alignment scores.
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To introduce PAM and BLOSUM substitution matrices.
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To introduce HSSP-curves and multiple alignments.
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To introduce comparative modelling and fold recognition.
Objectives
After this lecture you will be able to:
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compute z-scores to assess the significance of
global pairwise alignment scores;
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explain why substitution matrices and non-linear gap penalties can
produce better alignments;
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discuss how structural and functional clues can be inferred from
multiple alignments;
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describe how sequence identity and structure similarity are related;
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discuss the objectives of comparative modelling and fold recognition.
Supplementary Material
Some of the lecture slides are available on-line
(one per page,
four-per-page).
HSSP-curves were proposed by
Sander, C. and Schneider, R.
(Database of homology-derived protein structures and the structural meaning
of sequence alignment.
Proteins, 9, 56-68, 1991,
doi:10.1002/prot.340090107)
and were revised by:
Rost, B.
(Twilight zone of protein sequence alignments.
Protein Eng., 12, 85-94, 1999.
doi:10.1093/protein/12.2.85)
Some useful bioinformatics resources:
Last Modified: 7 November 2014
by Graham Kemp