1 / 35

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.

nerice
Download Presentation

Multiple Sequence Alignment

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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.

More Related