1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.
-
Upload
jesse-fitzgerald -
Category
Documents
-
view
272 -
download
9
Transcript of 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.
![Page 1: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/1.jpg)
1
Multiple Sequence Alignment
暨南大學資訊工程學系黃光璿2004/05/31
![Page 2: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/2.jpg)
2
What is a multiple alignment?
![Page 3: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/3.jpg)
3
![Page 4: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/4.jpg)
4
An alignment of ten I-set immunoglobin superfamily
![Page 5: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/5.jpg)
5
Motivation
A multiple alignment may suggest a common structure of the protein produ
cts; a common function; a common evolutionary source.
![Page 6: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/6.jpg)
6
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
![Page 7: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/7.jpg)
7
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.
![Page 8: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/8.jpg)
8
![Page 9: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/9.jpg)
9
![Page 10: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/10.jpg)
10
![Page 11: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/11.jpg)
11
![Page 12: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/12.jpg)
12
To prove that a computational problem is NP-hard, we need to reduce an NP-complete (hard) problem to
this problem.
![Page 13: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/13.jpg)
13
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
![Page 14: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/14.jpg)
14
![Page 15: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/15.jpg)
15
![Page 16: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/16.jpg)
16
![Page 17: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/17.jpg)
17
![Page 18: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/18.jpg)
18
![Page 19: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/19.jpg)
19
![Page 20: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/20.jpg)
20
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.
![Page 21: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/21.jpg)
21
![Page 22: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/22.jpg)
22
![Page 23: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/23.jpg)
23
![Page 24: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/24.jpg)
24
![Page 25: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/25.jpg)
25
![Page 26: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/26.jpg)
26
![Page 27: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/27.jpg)
27
![Page 28: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/28.jpg)
28
![Page 29: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/29.jpg)
29
![Page 30: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/30.jpg)
30
![Page 31: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/31.jpg)
31
![Page 32: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/32.jpg)
32
![Page 33: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/33.jpg)
33
![Page 34: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/34.jpg)
34
![Page 35: 1 Multiple Sequence Alignment 暨南大學資訊工程學系 黃光璿 2004/05/31.](https://reader033.fdocuments.net/reader033/viewer/2022061612/56649dd35503460f94aca974/html5/thumbnails/35.jpg)
35
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.