Multiple Sequence Alignment
暨南大學資訊工程學系
黃光璿
2004/05/31
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What is a multiple alignment?
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An alignment of ten I-set immunoglobin
superfamily
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Motivation
A multiple alignment may suggest

a common structure of the protein
products;
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a common function;
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a common evolutionary source.
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Issues

How to define meaningful scoring
function for an alignment?
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

evolutionary correct alignment --- more
difficult!
structure alignment
How to find the best alignment?

by algorithms
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Three types of alignment problems


DNA
protein


joined by disulfide bond
RNA

more difficult due to long-range correlation
We focus on alignment problems of
sequences of DNAs or proteins.
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
To prove that a computational problem
is NP-hard, we need

to reduce an NP-complete (hard) problem
to this problem.
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
When a computational problem is NPhard, we deal with it by



heuristic: convince other people by
experiments
approximation: how to analyze the
performance?
randomization: how to design a reasonable
algorithm
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Branch & bound heuristic for the DP
algorithm of the Sum-of-pairs


Carrillo & Lipman (1988)
The idea was implemented in the
famous problem MSA.
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
Lipman, Altshul, Kececiogly, 1989
MSA can align 6 sequences of length
~200 in reasonable time.
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參考資料及圖片出處
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Biological Sequence Analysis –
Probabilistic Models of Proteins and
Nucleic Acids
R. Durbin, S. Eddy, A. Krogh, and G.
Mitchison,
Cambridge University Press, 1998.
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