11. 2
Makorin1‐p1
Makorin1‐p1 ortholog rat
Makorin1‐p1
Mus musculus domes3cus 5
Subgenus
M. booduga
M. fragilicauda India+Lao/Thai
booduga
M. terricolor
1.5 M. macedonicus
4.3 mya M. spicilegus
mya
M. spretus
M. musculus castaneus
Palearctic
Mus
musculus
M. m. domesticus
M. m. molossinus
M. caroli
M. cookii Southeast Asia
M. cervicolor cervicolor
M. pahari Coelomys
M. mattheyi Nannomys
M. platythrix Pyromys
Apodemus agrarius
Micromys minutus
Rattus norvegicus (from Suzuki et al. 2004 Mol. Phylogenet. Evol.
0.01 33:626-646, Figure 1, 4.)
13. region B region C
regionB regionC number of differences p distance
region B bp
region C bp
pair
number of differences
p distance
number of differences
p distance
dom – mol
dom – cas
dom – mus
dom – spr
dom – car
mol ‐ cas
mol – mus
mol – spr
mol – car
cas – mus
cas – spr
cas – car
mus – spr
mus – car
spr – car
14. region B region C
Makorin1‐p1 (region B, regionC)
p distance
1) domesgcus Biostrings DNAstring
2) B
3) B
4) C
5) C
6) domesgcus DNAstring B C
7)
8) 4
16. Biostrings p distance 2
#Makorin1‐p1.fasta molossinus ””
# DNA mol
> mol <‐ DNAString("")
#mol 1 617 molB
> molB <‐ substring(mol,1,617)
#mol 618 1256 molC
> molC <‐ substring(mol, 618,1256)
# castaneus(cas), musculus(mus), spretus(spr), caroli(car)
# number of differences p distance
#
17. Biostrings p distance 3
> x <‐ domB
> y <‐ molB
# x y( domB molB)
> comp<‐ c(compareStrings(x,y))
# ? ?
> subt <‐ gsub("(['?'])", "", comp)
#subt DNA ide
> ide <‐ DNAString(subt)
#ide len
> len <‐ length(ide)
#x y dif
> dif <‐ (lengthB – len )
> dif #x y
#regionB p distance
> pdis <‐ dif/lengthB
> pdis #p distance 4
18. Biostrings p distance 4
CotEditor pdistanceB.R
[Macintosh HD/ /tg03/bin]
comp <‐ c(compareStrings(x,y))
2 lengthB lengthC
subt <‐ gsub("(['?'])", "", comp)
pdistanceC.R bin
ide <‐ DNAString(subt)
len <‐ length(ide)
dif <‐ (lengthB ‐ len)
pdis <‐ dif/lengthB
x y
> x <‐
> y <‐
> source("/Users/tg03/bin/pdistanceB.R")
bin
> source("pdistanceB.R")
2
> dif
> pdis
19. region B region C ( )
region B 617 bp
region C 639 bp
pair
number of differences
p distance
number of differences
p distance
dom – mol
6
0.010
7 0.011
dom – cas
6
0.010
7
0.011
dom – mus
8
0.013
8
0.013
dom – spr
16
0.026
14
0.022
dom – car
30
0.049
39
0.061
mol – cas
0
0
0
0
mol – mus
4
0.006
1
0.002
mol – spr
14
0.023
17
0.027
mol – car
28
0.045
38
0.059
cas – mus
4
0.006
1
0.002
cas – spr
14
0.023
17
0.027
cas – car
28
0.045
38
0.059
mus – spr
14
0.023
18
0.028
mus – car
28
0.045
39
0.061
spr – car
32
0.052
37
0.058
20. 1
1) regionB p distance x x
> x <‐ c(x )
2) regionC p distance y y
> y <‐ c(y )
3) x y
4) plot()
> plot(x,y,xlim=c( , ), ylim=c( , ))
21. 1
1) regionB p distance x x
> x <‐ c(0.010, 0.010, 0.013, 0.026, 0.049, 0, 0.006 ,0.023, 0.045, 0.006 , 0.023 , 0.045,
0.023, 0.045, 0.052 )
2) regionC p distance y y
> y <‐ c(0.011, 0.011, 0.013, 0.022, 0.061, 0, 0.002, 0.027, 0.059, 0.002, 0.027, 0.059,
0.028, 0.061, 0.058 )
3) max() x y
> max(x)
[1] 0.052
> max(y)
[1] 0.061
4) plot()
> plot(x,y,xlim=c(0,0.065), ylim=c(0,0.065))