Download Biological Sequence Analysis Project 2 Mid

Biological Sequence Analysis
Project 2 Mid-term Presentation
Exercise 1
2001-20546 한기혁
Multiple sequence alignment
• Target domain : protein C2 domain 1 from pfam database
1) seed 437 sequences
2) full 1087 sequences
Exercise 2
Make HMM
Exercise 3
Search the SWISS-PROT with HMM
1) seed
2) full
Exercise 4
Sequence
Description
Score E-value N
SY63_DISOM Synaptotagmin C (Synaptic vesicle protein 277.9 2.2e-79 2
SYT3_HUMAN Synaptotagmin III (SytIII).
233.6
5e-66 2
Calibrate HMM
• HMMER cyg/win problem – stack error
Exercise 5
Make HMM database
• Myhmms : C2 domain + pkinase protein kainase catalytic domain
Exercise 6
Parse the domain structure of a sequence with HMM database
• Target sequence : Schizosaccharomyces pombe Protein Kinase C-like 1
(PCK1_SCHPO (P36582))
1) seed
2) full
Exercise 7
Model
Domain seq-f seq-t hmm-f hmm-t
pc2dseed 1/1
212 292 .. 1
88 []
pkinase
1/1
664 923 .. 1
278 []
pc2dfull
1/1
212 292 .. 1
200 []
pkinase
1/1
664 923 .. 1
278 []
score
8.6
280.8
19.9
280.8
E-value
8.2e-06
6.1e-85
1.2e-06
6.1e-85
Search for domains of target sequence in PFAM database
Model
HR1
3-alpha
Upf2
Histone_HNS
HR1
IL8
PAH
C2
Atrophin-1
UPF0154
Phosphoprotein
DUF379
DAG_PE-bind
PHD
zf-C3HC4
TNFR_c6
fer4
DUF139
zf-NF-X1
DAG_PE-bind
zf-A20
DC1
DNA_RNApol_7kD
DUF359
MAT_Alpha1
pkinase
ATP-sulfurylase
DUF402
L27
pkinase_C
Domain
1/2
1/1
1/1
1/1
2/2
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/2
1/1
1/1
1/1
1/1
1/1
1/1
2/2
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
1/1
seq-f seq-t hmm-f hmm-t score E-value
6 78 ..
1 87 [] 17.6 0.0077
20 64 ..
1 49 [] -4.2
8.3
64 215 .. 1 202 [] -78.9
4.3
117 222 .. 1 130 [] -75.1
3.6
119 192 .. 1 87 [] 98.1 1.4e-26
126 176 .. 1 70 [] -27.6
9.3
132 174 .. 1 47 [] -10.4
7
212 292 .. 1 88 [] 8.6 0.0028
213 943 .. 1 1046 [] -749.7
8.4
374 432 .. 1 64 [] -23.7
3.1
402 694 .. 1 316 [] -145.6
9.1
406 476 .. 1 92 [] -39.3
4.8
414 461 .. 1 51 [] 68.5 1.2e-17
426 464 .. 1 51 [] 6.8 0.0013
427 461 .. 1 50 [] -18.7
5.7
430 469 .. 1 42 [] -8.3
5.1
434 455 .. 1 24 [] -8.3
4.3
440 455 .. 1 17 [] -3.1
6.7
442 463 .. 1 23 [] -4.0
6.5
481 530 .. 1 51 [] 65.0 1.3e-16
491 513 .. 1 26 [] -4.2
6.7
492 523 .. 1 44 [] 0.2
1
494 521 .. 1 32 [] 1.5 0.38
555 701 .. 1 176 [] -89.9
6.5
558 733 .. 1 214 [] -69.9
5.4
664 923 .. 1 294 [] 276.3 3.3e-80
668 903 .. 1 349 [] -197.9
1.9
716 821 .. 1 105 [] -25.9
2.2
891 942 .. 1 56 [] -6.6
8.1
924 988 .] 1 70 [] 125.0 1.1e-34
Discussion
• Target domain and sequence
: Clock-related gene
(BMAL, Clock, Per, DBP, etc)
• Project 1 – HMM model