11 Ch6 multiple sequence alignment methods 1 Biologists produce high quality multiple sequence...
-
date post
20-Dec-2015 -
Category
Documents
-
view
247 -
download
0
Transcript of 11 Ch6 multiple sequence alignment methods 1 Biologists produce high quality multiple sequence...
![Page 1: 11 Ch6 multiple sequence alignment methods 1 Biologists produce high quality multiple sequence alignment by hand using knowledge of protein sequence evolution.](https://reader036.fdocuments.net/reader036/viewer/2022081506/56649d445503460f94a21605/html5/thumbnails/1.jpg)
11
Ch6 multiple sequence alignment methods
1
Biologists produce high quality multiple sequence alignment by hand usingknowledge of protein sequence evolution.
Automatic multiple sequence alignment?-in probabilistic modeling, scoring function is primary concern, not the alignment algorithm
![Page 2: 11 Ch6 multiple sequence alignment methods 1 Biologists produce high quality multiple sequence alignment by hand using knowledge of protein sequence evolution.](https://reader036.fdocuments.net/reader036/viewer/2022081506/56649d445503460f94a21605/html5/thumbnails/2.jpg)
2
6.1 What a multiple alignment means
![Page 3: 11 Ch6 multiple sequence alignment methods 1 Biologists produce high quality multiple sequence alignment by hand using knowledge of protein sequence evolution.](https://reader036.fdocuments.net/reader036/viewer/2022081506/56649d445503460f94a21605/html5/thumbnails/3.jpg)
3
![Page 4: 11 Ch6 multiple sequence alignment methods 1 Biologists produce high quality multiple sequence alignment by hand using knowledge of protein sequence evolution.](https://reader036.fdocuments.net/reader036/viewer/2022081506/56649d445503460f94a21605/html5/thumbnails/4.jpg)
4
• In principle, there is always an unambiguously correct evolutionary alignment even if the structures diverge
• In practice, an evolutionarily correct alignment can be more difficult to infer than structural alignment
• Our ability to define a single ‘correct’ alignment will vary with the relatedness of the sequences being aligned
• Usually, a small subset of key residues will be identifiable which can be aligned unambiguously almost regardless of the sequence divergence
• We should focus on the subset of columns corresponding to key residues and core structural elements that can be aligned with confidence
![Page 5: 11 Ch6 multiple sequence alignment methods 1 Biologists produce high quality multiple sequence alignment by hand using knowledge of protein sequence evolution.](https://reader036.fdocuments.net/reader036/viewer/2022081506/56649d445503460f94a21605/html5/thumbnails/5.jpg)
5
![Page 6: 11 Ch6 multiple sequence alignment methods 1 Biologists produce high quality multiple sequence alignment by hand using knowledge of protein sequence evolution.](https://reader036.fdocuments.net/reader036/viewer/2022081506/56649d445503460f94a21605/html5/thumbnails/6.jpg)
6
![Page 7: 11 Ch6 multiple sequence alignment methods 1 Biologists produce high quality multiple sequence alignment by hand using knowledge of protein sequence evolution.](https://reader036.fdocuments.net/reader036/viewer/2022081506/56649d445503460f94a21605/html5/thumbnails/7.jpg)
7
![Page 8: 11 Ch6 multiple sequence alignment methods 1 Biologists produce high quality multiple sequence alignment by hand using knowledge of protein sequence evolution.](https://reader036.fdocuments.net/reader036/viewer/2022081506/56649d445503460f94a21605/html5/thumbnails/8.jpg)
8
![Page 9: 11 Ch6 multiple sequence alignment methods 1 Biologists produce high quality multiple sequence alignment by hand using knowledge of protein sequence evolution.](https://reader036.fdocuments.net/reader036/viewer/2022081506/56649d445503460f94a21605/html5/thumbnails/9.jpg)
9
6.3 Multidimensional dynamic programming
![Page 10: 11 Ch6 multiple sequence alignment methods 1 Biologists produce high quality multiple sequence alignment by hand using knowledge of protein sequence evolution.](https://reader036.fdocuments.net/reader036/viewer/2022081506/56649d445503460f94a21605/html5/thumbnails/10.jpg)
10
![Page 11: 11 Ch6 multiple sequence alignment methods 1 Biologists produce high quality multiple sequence alignment by hand using knowledge of protein sequence evolution.](https://reader036.fdocuments.net/reader036/viewer/2022081506/56649d445503460f94a21605/html5/thumbnails/11.jpg)
11
MSA (Carrillo & Lipman)
![Page 12: 11 Ch6 multiple sequence alignment methods 1 Biologists produce high quality multiple sequence alignment by hand using knowledge of protein sequence evolution.](https://reader036.fdocuments.net/reader036/viewer/2022081506/56649d445503460f94a21605/html5/thumbnails/12.jpg)
12
![Page 13: 11 Ch6 multiple sequence alignment methods 1 Biologists produce high quality multiple sequence alignment by hand using knowledge of protein sequence evolution.](https://reader036.fdocuments.net/reader036/viewer/2022081506/56649d445503460f94a21605/html5/thumbnails/13.jpg)
13
6.4 Progressive alignment methods
![Page 14: 11 Ch6 multiple sequence alignment methods 1 Biologists produce high quality multiple sequence alignment by hand using knowledge of protein sequence evolution.](https://reader036.fdocuments.net/reader036/viewer/2022081506/56649d445503460f94a21605/html5/thumbnails/14.jpg)
14
![Page 15: 11 Ch6 multiple sequence alignment methods 1 Biologists produce high quality multiple sequence alignment by hand using knowledge of protein sequence evolution.](https://reader036.fdocuments.net/reader036/viewer/2022081506/56649d445503460f94a21605/html5/thumbnails/15.jpg)
15
Profile alignment
![Page 16: 11 Ch6 multiple sequence alignment methods 1 Biologists produce high quality multiple sequence alignment by hand using knowledge of protein sequence evolution.](https://reader036.fdocuments.net/reader036/viewer/2022081506/56649d445503460f94a21605/html5/thumbnails/16.jpg)
16
CLUSTALW
![Page 17: 11 Ch6 multiple sequence alignment methods 1 Biologists produce high quality multiple sequence alignment by hand using knowledge of protein sequence evolution.](https://reader036.fdocuments.net/reader036/viewer/2022081506/56649d445503460f94a21605/html5/thumbnails/17.jpg)
17
![Page 18: 11 Ch6 multiple sequence alignment methods 1 Biologists produce high quality multiple sequence alignment by hand using knowledge of protein sequence evolution.](https://reader036.fdocuments.net/reader036/viewer/2022081506/56649d445503460f94a21605/html5/thumbnails/18.jpg)
18
Iterative refinement methods
![Page 19: 11 Ch6 multiple sequence alignment methods 1 Biologists produce high quality multiple sequence alignment by hand using knowledge of protein sequence evolution.](https://reader036.fdocuments.net/reader036/viewer/2022081506/56649d445503460f94a21605/html5/thumbnails/19.jpg)
19
6.5 Multiple alignment by profile HMM
![Page 20: 11 Ch6 multiple sequence alignment methods 1 Biologists produce high quality multiple sequence alignment by hand using knowledge of protein sequence evolution.](https://reader036.fdocuments.net/reader036/viewer/2022081506/56649d445503460f94a21605/html5/thumbnails/20.jpg)
20
![Page 21: 11 Ch6 multiple sequence alignment methods 1 Biologists produce high quality multiple sequence alignment by hand using knowledge of protein sequence evolution.](https://reader036.fdocuments.net/reader036/viewer/2022081506/56649d445503460f94a21605/html5/thumbnails/21.jpg)
21
![Page 22: 11 Ch6 multiple sequence alignment methods 1 Biologists produce high quality multiple sequence alignment by hand using knowledge of protein sequence evolution.](https://reader036.fdocuments.net/reader036/viewer/2022081506/56649d445503460f94a21605/html5/thumbnails/22.jpg)
22
![Page 23: 11 Ch6 multiple sequence alignment methods 1 Biologists produce high quality multiple sequence alignment by hand using knowledge of protein sequence evolution.](https://reader036.fdocuments.net/reader036/viewer/2022081506/56649d445503460f94a21605/html5/thumbnails/23.jpg)
23