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Multiple Sequence Alignment

Multiple Sequence Alignment. 暨南大學資訊工程學系 黃光璿 2004/05/31. What is a multiple alignment?. An alignment of ten I-set immunoglobin superfamily. Motivation. A multiple alignment may suggest a common structure of the protein products; a common function; a common evolutionary source. Issues.

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Multiple Sequence Alignment

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  1. Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31

  2. What is a multiple alignment?

  3. An alignment of ten I-set immunoglobin superfamily

  4. Motivation A multiple alignment may suggest • a common structure of the protein products; • a common function; • a common evolutionary source.

  5. 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

  6. 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.

  7. To prove that a computational problem is NP-hard, we need • to reduce an NP-complete (hard) problem to this problem.

  8. When a computational problem is NP-hard, we deal with it by • heuristic: convince other people by experiments • approximation: how to analyze the performance? • randomization: how to design a reasonable algorithm

  9. Branch & bound heuristic for the DP algorithm of the Sum-of-pairs • Carrillo & Lipman (1988) • The idea was implemented in the famous problem MSA. • Lipman, Altshul, Kececiogly, 1989 • MSA can align 6 sequences of length ~200 in reasonable time.

  10. 參考資料及圖片出處 • Biological Sequence Analysis – Probabilistic Models of Proteins and Nucleic AcidsR. Durbin, S. Eddy, A. Krogh, and G. Mitchison,Cambridge University Press, 1998.

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