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