a
--ここから---
swissprot:PRIO_HUMAN
swissprot:PRIO_RAT
swissprot:PRIO_MOUSE
swissprot:PRIO_CALJA
swissprot:PRIO_CANFA
swissprot:PRIO_BOVIN
swissprot:PRIO_AILME
swissprot:PRIO_CAPHI
swissprot:PRIO_SHEEP
swissprot:PRIO_CHICK
--ここまで--
Esc
:wq
$seqret @prion_names.txt -outseq=prion.fasta
$ grep ">" prion.fasta | cut -f1,2 -d" "
>PRIO_HUMAN P04156
>PRIO_RAT P13852
>PRIO_MOUSE P04925
>PRIO_CALJA P40247
>PRIO_CANFA O46501
>PRIO_BOVIN P10279
>PRIO_AILME Q6EH52
>PRIO_CAPHI P52113
>PRIO_SHEEP P23907
>PRIO_CHICK P27177
$sudo apt-get install clustalw
$clustalw prion.fasta
kappa@kappa-desktop:~/2011$ more prion.aln
CLUSTAL 2.0.10 multiple sequence alignment
PRIO_HUMAN --MANLGCWMLVLFVATWSDLGLCKK-RPKP-GG-WNTGGSR---YPGQ-GSPGGNRYPP
PRIO_CALJA --MANLGCWMLFLFVATWSDLGLCKK-RPKP-GG-WNTGGSR---YPGQ-GSPGGNRYPP
PRIO_RAT --MANLGYWLLALFVTTCTDVGLCKK-RPKP-GG-WNTGGSR---YPGQ-GSPGGNRYPP
PRIO_MOUSE --MANLGYWLLALFVTMWTDVGLCKK-RPKP-GG-WNTGGSR---YPGQ-GSPGGNRYPP
PRIO_BOVIN MVKSHIGSWILVLFVAMWSDVGLCKK-RPKP-GGGWNTGGSR---YPGQ-GSPGGNRYPP
PRIO_AILME MVKSHIGSWILVLFVAMWSDVGLCKK-RPKP-GGGWNTGGSR---YPGP-GSPGGNRYPP
PRIO_CAPHI MVKSHIGSWILVLFVAMWSDVGLCKK-RPKP-GGGWNTGGSR---YPGQ-GSPGGNRYPP
PRIO_SHEEP MVKSHIGSWILVLFVAMWSDVGLCKK-RPKP-GGGWNTGGSR---YPGQ-GSPGGNRYPP
PRIO_CANFA MVKSHIGSWILVLFVAMWSDVGLCKK-RPKP-GGGWNTGGSR---YPGQ-GSPGGNRYPP
PRIO_CHICK MARLLTTCCLLALLLAACTDVALSKKGKGKPSGGGWGAGSHRQPSYPRQPGYPHNPGYPH
:* *::: :*:.*.** : ** ** *.:*. * ** * * . **
PRIO_HUMAN QGGGGWGQPHGGGWGQPHGGGWGQ----PHGG--------GWGQPHGGG-WGQGGGTHSQ
PRIO_CALJA QGGG-WGQPHGGGWGQPHGGGWGQ----PHGG--------GWGQPHGGG-WGQGGGTHSQ
PRIO_RAT QSGGTWGQPHGGGWGQPHGGGWGQ----PHGG--------GWGQPHGGG-WSQGGGTHNQ
PRIO_MOUSE Q-GGTWGQPHGGGWGQPHGGSWGQ----PHGG--------SWGQPHGGG-WGQGGGTHNQ
PRIO_BOVIN QGGGGWGQPHGGGWGQPHGGGWGQ----PHGGGWGQPHGGGWGQPHGGGGWGQGG-THGQ
PRIO_AILME QGGGGWGQPHGGGWGQPHGGGWGQ----PHGGGWGQPHGGGWGQPHGGGGWGQGG-THGQ
PRIO_CAPHI QGGGGWGQPHGGGWGQPHGGGWGQ----PHGG--------GWGQPHGGGGWGQGG-SHSQ
PRIO_SHEEP QGGGGWGQPHGGGWGQPHGGGWGQ----PHGG--------GWGQPHGGGGWGQGG-SHSQ
PRIO_CANFA QGGGGWGQPHGGGWGQPHGGGWGQ----PHGG--------GWGQPHGGGGWGQGG-THSQ
PRIO_CHICK NPGYPHNPGYPHNPGYPHNPGYPQNPGYPHNPG-----YPGWGQGYNPS---SGGSYHNQ
: * . : . * **. .: * **. .*** :. . .** *.*
PRIO_HUMAN WNKPSKP-KTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRY
PRIO_CALJA WNKPSKP-KTNMKHVAGAAAAGAVVGGLGGYMLGSAMSRPLIHFGNDYEDRYYRENMYRY
PRIO_RAT WNKPSKP-KTNLKHVAGAAAAGAVVGGLGGYMLGSAMSRPMLHFGNDWEDRYYRENMYRY
PRIO_MOUSE WNKPSKP-KTNLKHVAGAAAAGAVVGGLGGYMLGSAMSRPMIHFGNDWEDRYYRENMYRY
PRIO_BOVIN WNKPSKP-KTNMKHVAGAAAAGAVVGGLGGYMLGSAMSRPLIHFGSDYEDRYYRENMHRY
PRIO_AILME WNKPSKP-KTNMKHVAGAAAAGAVVGGLGGYMLGSAMSRPLIHFGSDYEDRYYRENMHRY
PRIO_CAPHI WNKPSKP-KTNMKHVAGAAAAGAVVGGLGGYMLGSAMSRPLIHFGNDYEDRYYRENMYRY
PRIO_SHEEP WNKPSKP-KTNMKHVAGAAAAGAVVGGLGGYMLGSAMSRPLIHFGNDYEDRYYRENMYRY
PRIO_CANFA WNKPSKP-KTNMKHVAGAAAAGAVVGGLGGYLLGSAMSRPLIHFGNDCEDRYYRENMYRY
PRIO_CHICK --KPWKPPKTNFKHVAGAAAAGAVVGGLGGYAMGRVMSGMNYHFDSPDEYRWWSENSARY
** ** ***:**:**************** :* .** **.. * *:: ** **
PRIO_HUMAN PNQVYYRPMDEYSNQNNFVHDCVNITIKQHTV-TTTTKGENFTETDVKMMERVVEQMCIT
PRIO_CALJA PNQVYYRPVDQYNNQNNFVHDCVNITIKQHTV-TTTTKGENFTETDVKMMERVVEQMCIT
PRIO_RAT PNQVYYRPVDQYSNQNNFVHDCVNITIKQHTV-TTTTKGENFTETDVKMMERVVEQMCVT
PRIO_MOUSE PNQVYYRPVDQYSNQNNFVHDCVNITIKQHTV-TTTTKGENFTETDVKMMERVVEQMCVT
PRIO_BOVIN PNQVYYRPVDQYSNQNNFVHDCVNITVKEHTV-TTTTKGENFTETDIKMMERVVEQMCIT
PRIO_AILME PNQVYYRPVDQYSNQNNFVHDCVNITVKEHTV-TTTTKGENFTETDIKMMERVVEQMCIT
PRIO_CAPHI PNQVYYRPVDQYSNQNNFVHDCVNITVKQHTV-TTTTKGENFTETDIKIMERVVEQMCIT
PRIO_SHEEP PNQVYYRPVDRYSNQNNFVHDCVNITVKQHTV-TTTTKGENFTETDIKIMERVVEQMCIT
PRIO_CANFA PNQVYYRSVDQYNNQSTFVHDCVNITVKQHTV-TTT-KGENFTETDIKMMERVVEQMCIT
PRIO_CHICK PNRVYYRDYSSPVPQDVFVADCFNITVTEYSIGPAAKKNTSEAVAAANQTEVEMENKVVT
**:**** . *. ** **.***:.:::: .:: *. . : : : * :*: :*
PRIO_HUMAN QYERES--QAYYQ--RGSSMVLFSSP---PVILLISFLIFLIVG
PRIO_CALJA QYEKES--QAYYQ--RGSSMVLFSSP---PVILLISFLIFLIVG
PRIO_RAT QYQKES--QAYYDGRRSS-AVLFSSP---PVILLISFLIFLIVG
PRIO_MOUSE QYQKES--QAYYDGRRSSSTVLFSSP---PVILLISFLIFLIVG
PRIO_BOVIN QYQRES--QAYYQ--RGASVILFSSP---PVILLISFLIFLIVG
PRIO_AILME QYQRES--QAYYQ--RGASVILFSSP---PVILLISFLIFLIVG
PRIO_CAPHI QYQRES--QAYYQ--RGASVILFSPP---PVILLISFLIFLIVG
PRIO_SHEEP QYQRES--QAYYQ--RGASVILFSSP---PVILLISFLIFLIVG
PRIO_CANFA QYQRES--EAYYQ--RGASVILFSSP---PVILLVSFLIFLIVG
PRIO_CHICK KVIREMCVQQYREYRLASGIQLHPADTWLAVLLLLLTTLFAMH-
: :* : * : .: *... .*:**: :* :
#これは、美しい！！！！！今までGUIでclustalwをせっせとやっていたから驚きはでかい。
#Rの中で系統樹作成用のパッケージを読み込んで、系統樹を書かせてみる。
$sudo R
> install.packages("seqinr")
> install.packages("ape", dep=T)
> library(ape)
> library(seqinr)
> prion_align <- read.alignment(file="prion.aln",format="clustal")
> plot(nj(dist.alignment(prion_align)))
> plot(nj(dist.alignment(prion_align)), type = "unrooted")
#驚くほど綺麗な絵になったので保存しとく。
> png("110128_phyl.png")
> par(mfrow=c(1,2))
> plot(nj(dist.alignment(prion_align)))
> plot(nj(dist.alignment(prion_align)), type = "unrooted")
> dev.off()
今日はバイオインフォマティクスって感じのプログラムの勉強ができた☆
