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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 produ

cts; a common function; a common evolutionary source.

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Issues

How to define meaningful scoring function for an alignment? 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 NP-hard, we deal with it by heuristic: convince other people by experiment

s approximation: how to analyze the performanc

e? randomization: how to design a reasonable alg

orithm

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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 p

roblem MSA. 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

1. Biological Sequence Analysis – Probabilistic Models of Proteins and Nucleic AcidsR. Durbin, S. Eddy, A. Krogh, and G. Mitchison,

Cambridge University Press, 1998.