1. 20
DB
2008/08/12
kaneko.satoko(at)ocha.ac.jp

4. ATGC
Figure
Figure 4-5 Molecular Biology of the Cell (© Garland Science 2008)

5. 3%
junk DNA
junk DNA
Figure
Figure 4-17 Molecular Biology of the Cell (© Garland Science 2008)

6. C
α
T
β
β
β
β
A
T
Figure
α
A
G
α
:transition
β
:transversion
G
C
purine
pyrimidine
Figure 4‐4 Molecular Biology of the Cell (© Garland Science 2008)

7. (polymorphism) (substitution)
1 (mutation)
(advantageous) (neutral) (deleterious)

8. ( )
( )
10 20
T······A·· ······C··G
·······A·· ·C····C··G
T······A·· ······C··G
T······A·· ·C····C···
····C··A·· ······C···
CAGGGCATCC GTCCTCGCCA
·TC······· ····C···G·
·T·······T ····C·····
·T·······T ····C··C··
·T····T··T ····C·····
·T········ ····C···G·

10. TCAGTGACCT
TCTGTCACGT
TCTGTGACCT
6th G C
3th T A 9th C G
TCAGTGACCT
TCTGTCACGT

11. ATGC 4
1
2
TCTGAGACCT
TCTGTGACCT
5th A T 6th G C
3th T A 6th G C
6th G C
3th T A
9th C G 9th C G
5th A T 6th C G
TCAGTGACCT
TCTGTCACGT
TCAGTGACCT
TCTGTCACGT
Jukes and Cantor (1969) Kimura 2-parameter(1980)

12. Coding Sequence 2

13. 1st (Leu, Arg)
2nd
3rd transition

14. synonymous substitution S
nonsynonymous substitution N
a) TCA TCT Ser
a)
T
Ser
2 C
Ser 0/2 1/1
3 A T Ser N S
b)
c)
b) Leu Arg 6
1
( )
c) 0/1 2/2
/ N S

15. 2
( )
d)
1/4 CAT CGG
1/4 2
N
N
CGT CAG
2 4
1/4 1/4
S
N
d) 1/4x2=0.5
1( 1 )+3/4x2=2.5
e)
f)
e)
1/4
1/4 1/4
1/4 (1/4+1/4)x2=1
N
S
N
N
1( 2 )+
(1/4+1/4)x2=2
1/4 1/4 1/4 1/4 f)
S
N
N
N

16. []
S N

17. []
S N
6

18. ( )
2
a)
b)
c)

19. a)
b)
c)
1/4
1/4 1/4
1/4 1/4
1/4
S
N
N
S
N
N
1/4 1/4 1/4 1/4
1/4 1/4
S
N
N
N
N
S
:(1/4+1/4)x2 = :0
(1/4+1/4)x2+1 = :3
:(1/4+1/4)x2 =
(1/4+1/4)x2+1 =

20. NJ (Neighbor-Joining)
MP (maximum parsimony)
ML (maximum likelihood
S.

21. seq1
seq2
seq3
seq4
seq1
2
seq2
0.2
seq3
seq4

22. seq1
seq2
seq3
seq4
seq1
seq2
0.2
seq3
0.1
0.3
seq4
0.4
0.4
0.5
seq1
0.1

23. seq1
seq2
seq3
seq4
seq1
seq2
0.2
seq3
0.1
0.3
seq4
0.4
0.4
0.5
seq2
(0.1)
seq1
(0.1)
(0.1)
(0.3)
seq3
seq4
0.1

24. seq1
seq2
seq3
seq4
seq5
seq6
seq1
seq2
0.2
seq3
0.1
0.3
seq4
0.3
0.3
0.4
seq5
0.2
0.4
0.3
0.5
seq6
0.2
0.4
0.3
0.5
0.2
seq1
0.1

25. seq1
seq2
seq3
seq4
seq5
seq6
seq1
seq2
0.2
seq3
0.1
0.3
seq4
0.3
0.3
0.4
seq5
0.2
0.4
0.3
0.5
seq6
0.2
0.4
0.3
0.5
0.2
seq6
seq5
(0.1)
seq2
(0.1)
(0.1)
seq1
(0.1)
(0.1)
(0.1)
(0.2)
seq3
seq4
0.1

26. 1
2

27. 3
4

28. node

29. 3

31. -Rhodopsin -
Forward strand 6.70kb

32. CLC Sequence Viewer
CLC Sequence Viewer (Free)
http://www.clcbio.com/index.php?id=910
Installer
Installer( )

33. CLC Sequence Viewer
CLC Sequence Viewer 5 Plug-ins and Resources Download
Plug-ins Additional Alignments
ClustalW

34. CLC Sequence Viewer
ClustalW
CLC_Data Rhodopsin

35. NCBI
Search NCBI
[All Fields] [Definition/Title] Rhodopsin
Add search parameter [Organism] human
human NM_000539, chimpanzee XM_516740,
rhesus monkey XM_001094250

36. Download and Save
OK
Accession number

37. Annotation layout Show annotation
Annotatioin types CDS
CDS
Delete
Selection

38. ClustalW alignment
Tool box Additional Alignment ClustalW
alignment Next parameter
Gaps Custom gap open penalty
Make a phylogenetic tree( )
alignment check Finish

39. Gap penalty

40. Alignment
alignment
(human, chimpanzee, rhesus monkey )

41. [.aln]
Export Format Clustal Alignment (.aln)
alignment
Export

42. transition/transversion
Rhodopsin CDS(coding sequence) 1047bp
transition: A G, C T
transversion: A,G C,T
human – chimpanzee, human – macaque
(NM_000539)-(XM_516740) (NM_000539)-(XM_001094250)
transition transversion
p-distace
p-distance = /
transi?on
transversion
p‐distance (%)
human‐
chimpanzee
human‐
macaque

43. Rhodopsin CDS(coding sequence) 1047bp
transition: A G, C T
transversion: A,G C,T
human – chimpanzee, human – macaque
(NM_000539)-(XM_516740) (NM_000539)-(XM_001094250)
transition transversion
transi?on
transversion
p‐distance (%)
human‐
5
1
6/1047 = 0.5
chimpanzee
human‐
31
9
40/1047 = 3.8
macaque
600
2500

44. Rhodopsin
rhesus monkey
rabbit
harp seal
manatee
dolphin
elephant
dannart (Marsupial)
platypus (Monotreme)
NJ tree bootstrap
distance:Modified Nei&Gojobori Nonsynonymous(p-distance)
number of sites:738
cod
finch

45. NCBI
Accession number
Search Nucleotide for Accession number Accession number

46. alignment
Toolbox Create Tree alignment
Next

47. ( )
Neighbor joining Bootstrap 1000
Bootstrap
OTU

48. Rhodopsin
alignment
1)
/ /
2) alignment insertion( ) deletion( )
3)
4)

49. 20 DB