---[p.57]------------------------------------------------------------
Chap.3 Sequence Analysis with R
データベースから配列を取得するのに"SeqinR"ライブラリを使います。
詳しくはこちらを参照＞ http://seqinr.r-forge.r-project.org/
> install.packages("seqinr")
> 略
>
> library(seqinr)
>
> choosebank() ネットワーク次第でうまくいかない場合有。数回トライ
[1] "genbank" "embl" "emblwgs" "swissprot"
[5] "ensembl" "hogenom" "hogenomdna" "hovergendna"
[9] "hovergen" "hogenom5" "hogenom5dna" "hogenom4"
[13] "hogenom4dna" "homolens" "homolensdna" "hobacnucl"
[17] "hobacprot" "phever2" "phever2dna" "refseq"
[21] "greviews" "bacterial" "archaeal" "protozoan"
[25] "ensprotists" "ensfungi" "ensmetazoa" "ensplants"
[29] "ensemblbacteria" "mito" "polymorphix" "emglib"
[33] "refseqViruses" "taxodb"
> ?choosebank
>
>
> choosebank("genbank")
>
> t1 <- query("BRCA1","SP=Homo sapiens AND K=BRCA1") 注）本と異なる
>
>
> attributes(t1)
$names
[1] "call" "name" "nelem" "typelist" "req" "socket"
$class
[1] "qaw"
>
> summary(t1)
Length Class Mode
call 3 -none- call
name 1 -none- character
nelem 1 -none- numeric
typelist 1 -none- character
req 158 -none- list
socket 1 sockconn numeric
>
>
> t1$name
[1] "BRCA1"
>
> t1$req
[[1]]
name length frame ncbicg
"AB621825.BRCA1" "71" "0" "1"
[[2]]
name length frame ncbicg
"AF005068.BRCA1" "5379" "0" "1"
＜中略＞
[[158]]
name length frame ncbicg
"Y08757.BRCA1" "88" "0" "1"
>
> t2<-query(listname="BRCA1", query="SP=Homo sapiens AND AC=U61268")
>
> t2
1 SQ for SP=Homo sapiens AND AC=U61268
>
>
> summary(t2)
Length Class Mode
call 3 -none- call
name 1 -none- character
nelem 1 -none- numeric
typelist 1 -none- character
req 1 -none- list
socket 1 sockconn numeric
>
>
>
>
> t1_seq1 <- getSequence(t1$req[[1]])
>
> t1_seq1
[1] "a" "t" "g" "g" "a" "t" "t" "t" "a" "t" "c" "t" "g" "c" "t" "c" "t" "t"
[19] "c" "g" "c" "g" "t" "t" "g" "a" "a" "g" "a" "a" "g" "t" "a" "c" "a" "a"
[37] "a" "a" "t" "g" "t" "c" "a" "t" "t" "a" "a" "t" "g" "c" "t" "a" "t" "g"
[55] "c" "a" "g" "a" "a" "a" "a" "t" "c" "t" "t" "a" "g" "a" "g" "t" "g"
>
>
> t2_seq1 <- getSequence(t2$req[[1]])
>
>
> t2_seq1
[1] "t" "c" "g" "c" "t" "a" "g" "a" "a" "c" "c" "c" "g" "g" "g" "a" "g" "g"
[19] "c" "g" "g" "a" "g" "g" "t" "t" "g" "c" "a" "g" "t" "g" "a" "g" "c" "c"
<中略>
[1315] "g" "a" "a" "a" "a" "c" "c" "c" "c" "c" "t" "c" "t" "c" "c" "a" "c" "t"
[1333] "a" "a" "a" "a" "a" "t"
> closebank()
>
> t1_ann1 <- getAnnot(t1$req[[1]]) closebankすると使えない
Error in summary.connection(socket) : invalid connection
>
> choosebank("genbank") 再開
>
>
> t1_ann1 <- getAnnot(t1$req[[1]]) 注釈データをダウンロード可能に
>
> t1_ann1
[1] " CDS 648..>718"
[2] " /gene=\"BRCA1\""
[3] " /codon_start=1"
[4] " /product=\"breast cancer type 1 susceptibility protein\""
[5] " /protein_id=\"BAK64160.1\""
[6] " /db_xref=\"GI:344179065\""
[7] " /translation=\"MDLSALRVEEVQNVINAMQKILE\""
>
--------------[p.63]-------------------------------------------------------------------------------------
FASTA形式ファイルの読込み
FASTA形式＝塩基配列・アミノ酸配列のファイル形式のスタンダード
https://en.wikipedia.org/wiki/FASTA_format
https://ja.wikipedia.org/wiki/FASTA
ファイル置き場
(1)入力ファイル
./data/myfasta.fasta
./data/MyBRCA.fasta
(2)出力ファイル
./data/myBRCA1to4.fa
> mysequence <- read.fasta(file="myfasta.fasta")
>
> mysequence
$`2BQ0:A|PDBID|CHAIN|SEQUENCE`
[1] "m" "t" "m" "d" "k" "s" "e" "l" "v" "q" "k" "a"
[13] "k" "l" "a" "e" "q" "a" "e" "r" "y" "d" "d" "m"
[25] "a" "a" "a" "m" "k" "a" "v" "t" "e" "q" "g" "h"
[37] "e" "l" "s" "n" "e" "e" "r" "n" "l" "l" "s" "v"
[49] "a" "y" "k" "n" "v" "v" "g" "a" "r" "r" "s" "s"
[61] "w" "r" "v" "i" "s" "s" "i" "e" "q" "k" "t" "e"
[73] "r" "n" "e" "k" "k" "q" "q" "m" "g" "k" "e" "y"
[85] "r" "e" "k" "i" "e" "a" "e" "l" "q" "d" "i" "c"
[97] "n" "d" "v" "l" "e" "l" "l" "d" "k" "y" "l" "i"
[109] "p" "n" "a" "t" "q" "p" "e" "s" "k" "v" "f" "y"
[121] "l" "k" "m" "k" "g" "d" "y" "f" "r" "y" "l" "s"
[133] "e" "v" "a" "s" "g" "d" "n" "k" "q" "t" "t" "v"
[145] "s" "n" "q" "q" "a" "y" "q" "e" "a" "f" "e" "i"
[157] "s" "k" "k" "e" "m" "q" "p" "t" "h" "p" "i" "r"
[169] "l" "g" "l" "a" "l" "n" "f" "s" "v" "f" "y" "y"
[181] "e" "i" "l" "n" "s" "p" "e" "k" "a" "c" "s" "l"
[193] "a" "k" "t" "a" "f" "d" "e" "a" "i" "a" "e" "l"
[205] "d" "t" "l" "n" "e" "e" "s" "y" "k" "d" "s" "t"
[217] "l" "i" "m" "q" "l" "l" "r" "d" "n" "l" "t" "w"
[229] "t" "s" "e" "n" "q" "g" "d" "e" "g" "e" "n" "l"
[241] "y" "f" "q"
attr(,"name")
[1] "2BQ0:A|PDBID|CHAIN|SEQUENCE"
attr(,"Annot")
[1] ">2BQ0:A|PDBID|CHAIN|SEQUENCE"
attr(,"class")
[1] "SeqFastadna"
>
> mynames <- getName(t1)
>
> mynames
[1] "AB621825.BRCA1" "AF005068.BRCA1"
[3] "AF284812.BRCA1" "AF507076.BRCA1"
[5] "AF507077.BRCA1" "AF507078.BRCA1"
[7] "AY093484.BRCA1" "AY093485.BRCA1"
[9] "AY093486.BRCA1" "AY093487.BRCA1"
[11] "AY093489.BRCA1" "AY093490.BRCA1"
[13] "AY093491.BRCA1" "AY093492.BRCA1"
[15] "AY093493.BRCA1" "AY144588"
[17] "AY150865" "AY273801.BRCA1"
[19] "AY304547.BRCA1" "AY438030"
[21] "AY438031" "AY706911"
[23] "AY706912.BRCA1" "AY706913"
[25] "AY751490" "BC030969.BRCA1"
[27] "BC062429" "BC072418.BRCA1"
[29] "BC085615.BRCA1" "BC106745.BRCA1"
[31] "BC106746" "BC115037.BRCA1"
[33] "DQ075361" "DQ116737"
[35] "DQ145822" "DQ145823"
[37] "DQ145824" "DQ145825.BRCA1"
[39] "DQ145826" "DQ190450.BRCA1"
[41] "DQ190451.BRCA1" "DQ190452.BRCA1"
[43] "DQ190453.BRCA1" "DQ190454.BRCA1"
[45] "DQ190455.BRCA1" "DQ190456.BRCA1"
[47] "DQ190457.BRCA1" "DQ299305"
[49] "DQ299306" "DQ299307"
[51] "DQ299308" "DQ299309"
[53] "DQ299310" "DQ299311"
[55] "DQ299312" "DQ299313"
[57] "DQ299314" "DQ299315"
[59] "DQ299316" "DQ299317"
[61] "DQ299318" "DQ299319"
[63] "DQ299320" "DQ299321"
[65] "DQ299322" "DQ299323"
[67] "DQ299324" "DQ299325"
[69] "DQ299326" "DQ299327"
[71] "DQ299328" "DQ299330"
[73] "DQ299331" "DQ363751.BRCA1"
[75] "DQ478408.BRCA1" "FJ940752.BRCA1"
[77] "HE600032" "HE600033.BRCA1"
[79] "HE600034" "HE600035"
[81] "HE600036" "HE600037"
[83] "HE600038" "HSU14680.BRCA1"
[85] "HSU18009" "HSU18018"
[87] "HSU37574.BRCA1" "HSU61268.BRCA1"
[89] "HSU64805" "HSU68041.BRCA1"
[91] "JN384124.BRCA1" "JN686490"
[93] "JX480460.BRCA1" "JX480461"
[95] "JX480462.BRCA1" "JX480463.BRCA1"
[97] "JX480464.BRCA1" "JX480465.BRCA1"
[99] "JX480466.BRCA1" "JX480467"
[101] "KJ625149.BRCA1" "KJ625150.BRCA1"
[103] "KJ625151.BRCA1" "KJ625152.BRCA1"
[105] "KJ625153.BRCA1" "KJ625154.BRCA1"
[107] "KJ625155.BRCA1" "KJ625156.BRCA1"
[109] "KJ625157.BRCA1" "KJ625158.BRCA1"
[111] "KJ625159.BRCA1" "KJ625160.BRCA1"
[113] "KJ625161.BRCA1" "KJ625162"
[115] "KJ625163.BRCA1" "KJ625164.BRCA1"
[117] "KJ625165.BRCA1" "KJ625166.BRCA1"
[119] "KJ625167.BRCA1" "KJ625168.BRCA1"
[121] "KJ625169.BRCA1" "KJ625170.BRCA1"
[123] "KJ625171.BRCA1" "KJ625172.BRCA1"
[125] "KJ625173.BRCA1" "KJ625174.BRCA1"
[127] "KJ625175.BRCA1" "KJ625176.BRCA1"
[129] "KJ625176.PE2" "KJ625177.BRCA1"
[131] "KJ625178.BRCA1" "KJ625179.BRCA1"
[133] "KM434065" "KP255396.BRCA1"
[135] "KP255397.BRCA1" "KP255398.BRCA1"
[137] "KP255399.BRCA1" "KP255400.BRCA1"
[139] "KP255401.BRCA1" "KP255402.BRCA1"
[141] "KP255403.BRCA1" "KP272102.BRCA1"
[143] "KP272103.BRCA1" "KP272104.BRCA1"
[145] "KP272105.BRCA1" "KP272106.BRCA1"
[147] "KP404097" "KP455327.BRCA1"
[149] "KP701015" "KP701016.BRCA1"
[151] "KP729136" "KP729137"
[153] "KP744861" "KP753383.BRCA1"
[155] "KT120061.BRCA1" "L78833.BRCA1"
[157] "S78558.BRCA1" "Y08757.BRCA1"
>
> length(t1)
[1] 6
>
> length(mynames)
[1] 158
>
> myseq.string <- getSequence(t1$req[1:4],as.string=TRUE)
>
> myseq.string
[[1]]
[1] "atggatttatctgctcttcgcgttgaagaagtacaaaatgtcattaatgctatgcagaaaatcttagagtg"
[[2]]
[1] "atgagcctacaagaaagtacgagattcagtcaacttgttgaagagctattgaaaaccatttgtgcttttcagcttgacacaggtttggagtatgcaaacagctataattttgcaaaaaaggaaaataactctcctgaacatctaaaagatgaagtttctatcatccaaagtatgggctacagaaaccgtgccaaaagacttctacagagtgaacccgaaaatccttccttggaaaccagtctcagtgtccaactctctaaccttggaactgtgagaactctgaggacaaagcagcggatacaacctcaaaagacgtctgtctacattgaattgggatctgattcttctgaagataccgttaataaggcaacttattgcagtgtgggagatcaagaattgttacaaatcacccctcaaggaaccagggatgaaatcagtttggactctgcaaaaaaggctgcttgtgaattttctgagacggatgtaacaaatactgaacatcatcaacccagtaataatgatttgaacaccactgagaagcgtgcagctgagaggcatccagaaaagtatcagggtagttctgtttcaaacttgcatgtggagccatgtggcacaaatactcatgccagctcattacagcatgagaacagcagtttattactcactaaagacagaatgaatgtagaaaaggctgaattctgtaataaaagcaaacagcctggcttagcaaggagccaacataacagatgggctggaagtaaggaaacatgtaatgataggcggactcccagcacagaaaaaaaggtagatctgaatgctgatcccctgtgtgagagaaaagaatggaataagcagaaactgccatgctcagagaatcctagagatactgaagatgttccttggataacactaaatagcagcattcagaaagttaatgagtggttttccagaagtgatgaactgttaggttctgatgactcacatgatggggagtctgaatcaaatgccaaagtagctgatgtattggacgttctaaatgaggtagatgaatattctggttcttcagagaaaatagacttactggccagtgatcctcatgaggctttaatatgtaaaagtgaaagagttcactccaaatcagtagagagtaatattgaagacaaaatatttgggaaaacctatcggaagaaggcaagcctccccaacttaagccatgtaactgaaaatctaattataggagcatttgttactgagccacagataatacaagagcgtcccctcacaaataaattaaagcgtaaaaggagacctacatcaggccttcatcctgaggattttatcaagaaagcagatttggcagttcaaaagactcctgaaatgataaatcagggaactaaccaaacggagcagaatggtcaagtgatgaatattactaatagtggtcatgagaataaaacaaaaggtgattctattcagaatgagaaaaatcctaacccaatagaatcactcgaaaaagaatctgctttcaaaacgaaagctgaacctataagcagcagtataagcaatatggaactcgaattaaatatccacaattcaaaagcacctaaaaagaataggctgaggaggaagtcttctaccaggcatattcatgcgcttgaactagtagtcagtagaaatctaagcccacctaattgtactgaattgcaaattgatagttgttctagcagtgaagagataaagaaaaaaaagtacaaccaaatgccagtcaggcacagcagaaacctacaactcatggaaggtaaagaacctgcaactggagccaagaagagtaacaagccaaatgaacagacaagtaaaagacatgacagcgatactttcccagagctgaagttaacaaatgcacctggttcttttactaagtgttcaaataccagtgaacttaaagaatttgtcaatcctagccttccaagagaagaaaaagaagagaaactagaaacagttaaagtgtctaataatgctgaagaccccaaagatctcatgttaagtggagaaagggttttgcaaactgaaagatctgtagagagtagcagtatttcattggtacctggtactgattatggcactcaggaaagtatctcgttactggaagttagcactctagggaaggcaaaaacagaaccaaataaatgtgtgagtcagtgtgcagcatttgaaaaccccaagggactaattcatggttgttccaaagataatagaaatgacacagaaggctttaagtatccattgggacatgaagttaaccacagtcgggaaacaagcatagaaatggaagaaagtgaacttgatgctcagtatttgcagaatacattcaaggtttcaaagcgccagtcatttgctccgttttcaaatccaggaaatgcagaagaggaatgtgcaacattctctgcccactctgggtccttaaagaaacaaagtccaaaagtcacttttgaatgtgaacaaaaggaagaaaatcaaggaaagaatgagtctaatatcaagcctgtacagacagttaatatcactgcaggctttcctgtggttggtcagaaagataagccagttgataatgccaaatgtagtatcaaaggaggctctaggttttgtctatcatctcagttcagaggcaacgaaactggactcattactccaaataaacatggacttttacaaaacccatatcgtataccaccactttttcccatcaagtcatttgttaaaactaaatgtaagaaaaatctgctagaggaaaactttgaggaacattcaatgtcacctgaaagagaaatgggaaatgagaacattccaagtacagtgagcacaattagccgtaataacattagagaaaatgtttttaaagaagccagctcaagcaatattaatgaagtaggttccagtactaatgaagtgggctccagtattaatgaaataggttccagtgatgaaaacattcaagcagaactaggtagaaacagaaggcccaaattgaatgctatgcttagattaggggttttgcaacctgaggtctataaacaaagtcttcctggaagtaattgtaagcatcctgaaataaaaaagcaagaatatgaagaagtagttcagactgttaatacagatttctctccatatctgatttcagataacttagaacagcctatgggaagtagtcatgcatctcaggtttgttctgagacacctgatgacctgttagatgatggtgaaataaaggaagatactagttttgctgaaaatgacattaaggaaagttctgctgtttttagcaaaagcgtccagaaaggagagcttagcaggagtcctagccctttcacccatacacatttggctcagggttaccgaagaggggccaagaaattagagtcctcagaagagaacttatctagtgaggatgaagagcttccctgcttccaacacttgttatttggtaaagtaaacaatataccttctcagtctactaggcatagcaccgttgctaccgagtgtctgtctaagaacacagaggagaatttattatcattgaagaatagcttaaatgactgcagtaaccaggtaatattggcaaaggcatctcaggaacatcaccttagtgaggaaacaaaatgttctgctagcttgttttcttcacagtgcagtgaattggaagacttgactgcaaatacaaacacccaggatcctttcttgattggttcttccaaacaaatgaggcatcagtctgaaagccagggagttggtctgagtgacaaggaattggtttcagatgatgaagaaagaggaacgggcttggaagaaaataatcaagaagagcaaagcatggattcaaacttaggtgaagcagcatctgggtgtgagagtgaaacaagcgtctctgaagactgctcagggctatcctctcagagtgacattttaaccactcagcagagggataccatgcaacataacctgataaagctccagcaggaaatggctgaactagaagctgtgttagaacagcatgggagccagccttctaacagctacccttccatcataagtgactcttctgcccttgaggacctgcgaaatccagaacaaagcacatcagaaaaagcagtattaacttcacagaaaagtagtgaataccctataagccagaatccagaaggcctttctgctgacaagtttgaggtgtctgcagatagttctaccagtaaaaataaagaaccaggagtggaaaggtcatccccttctaaatgcccatcattagatgataggtggtacatgcacagttgctctgggagtcttcagaatagaaactacccatctcaagaggagctcattaaggttgttgatgtggaggagcaacagctggaagagtctgggccacacgatttgacggaaacatcttacttgccaaggcaagatctagagggaaccccttacctggaatctggaatcagcctcttctctgatgaccctgaatctgatccttctgaagacagagccccagagtcagctcgtgttggcaacataccatcttcaacctctgcattgaaagttccccaattgaaagttgcagaatctgcccagagtccagctgctgctcatactactgatactgctgggtataatgcaatggaagaaagtgtgagcagggagaagccagaattgacagcttcaacagaaagggtcaacaaaagaatgtccatggtggtgtctggcctgaccccagaagaatttatgctcgtgtacaagtttgccagaaaacaccacatcactttaactaatctaattactgaagagactactcatgttgttatgaaaacagatgctgagtttgtgtgtgaacggacactgaaatattttctaggaattgcgggaggaaaatgggtagttagctatttctgggtgacccagtctattaaagaaagaaaaatgctgaatgagcatgattttgaagtcagaggagatgtggtcaatggaagaaaccaccaaggtccaaagcgagcaagagaatcccaggacagaaagatcttcagggggctagaaatctgttgctatgggcccttcaccaacatgcccacagatcaactggaatggatggtacagctgtgtggtgcttctgtggtgaaggagctttcatcattcacccttggcacaggtgtccacccaattgtggttgtgcagccagatgcctggacagaggacaatggcttccatgcaattgggcagatgtgtgaggcacctgtggtgacccgagagtgggtgttggacagtgtagcactctaccagtgccaggagctggacacctacctgataccccagatcccccacagccactactga"
[[3]]
[1] "catgattttgaagtcagaggagatgtggtcaatggaagaaaccaccaaggtccaaagcgagcaagagaatcccaggacagaaag"
[[4]]
[1] "catgattttgaagtcagaggagatgtggtcaatggaagaaaccaccaaggtccaaagcgagcaagagaatcccaggacagaaag"
> mynames<-getName(t1$req[1:4]) > > write.fasta(myseq.string,mynames,file.out="myBRCA1to4.fa")
■myBRCA1to4.faの中身は次の通りです
>AB621825.BRCA1
atggatttatctgctcttcgcgttgaagaagtacaaaatgtcattaatgctatgcagaaaatcttagagtg
>AF005068.BRCA1
atgagcctacaagaaagtacgagattcagtcaacttgttgaagagctattgaaaaccatttgtgcttttcagcttgacacaggtttggagtatgcaaacagctataattttgcaaaaaaggaaaataactctcctgaacatctaaaagatgaagtttctatcatccaaagtatgggctacagaaaccgtgccaaaagacttctacagagtgaacccgaaaatccttccttggaaaccagtctcagtgtccaactctctaaccttggaactgtgagaactctgaggacaaagcagcggatacaacctcaaaagacgtctgtctacattgaattgggatctgattcttctgaagataccgttaataaggcaacttattgcagtgtgggagatcaagaattgttacaaatcacccctcaaggaaccagggatgaaatcagtttggactctgcaaaaaaggctgcttgtgaattttctgagacggatgtaacaaatactgaacatcatcaacccagtaataatgatttgaacaccactgagaagcgtgcagctgagaggcatccagaaaagtatcagggtagttctgtttcaaacttgcatgtggagccatgtggcacaaatactcatgccagctcattacagcatgagaacagcagtttattactcactaaagacagaatgaatgtagaaaaggctgaattctgtaataaaagcaaacagcctggcttagcaaggagccaacataacagatgggctggaagtaaggaaacatgtaatgataggcggactcccagcacagaaaaaaaggtagatctgaatgctgatcccctgtgtgagagaaaagaatggaataagcagaaactgccatgctcagagaatcctagagatactgaagatgttccttggataacactaaatagcagcattcagaaagttaatgagtggttttccagaagtgatgaactgttaggttctgatgactcacatgatggggagtctgaatcaaatgccaaagtagctgatgtattggacgttctaaatgaggtagatgaatattctggttcttcagagaaaatagacttactggccagtgatcctcatgaggctttaatatgtaaaagtgaaagagttcactccaaatcagtagagagtaatattgaagacaaaatatttgggaaaacctatcggaagaaggcaagcctccccaacttaagccatgtaactgaaaatctaattataggagcatttgttactgagccacagataatacaagagcgtcccctcacaaataaattaaagcgtaaaaggagacctacatcaggccttcatcctgaggattttatcaagaaagcagatttggcagttcaaaagactcctgaaatgataaatcagggaactaaccaaacggagcagaatggtcaagtgatgaatattactaatagtggtcatgagaataaaacaaaaggtgattctattcagaatgagaaaaatcctaacccaatagaatcactcgaaaaagaatctgctttcaaaacgaaagctgaacctataagcagcagtataagcaatatggaactcgaattaaatatccacaattcaaaagcacctaaaaagaataggctgaggaggaagtcttctaccaggcatattcatgcgcttgaactagtagtcagtagaaatctaagcccacctaattgtactgaattgcaaattgatagttgttctagcagtgaagagataaagaaaaaaaagtacaaccaaatgccagtcaggcacagcagaaacctacaactcatggaaggtaaagaacctgcaactggagccaagaagagtaacaagccaaatgaacagacaagtaaaagacatgacagcgatactttcccagagctgaagttaacaaatgcacctggttcttttactaagtgttcaaataccagtgaacttaaagaatttgtcaatcctagccttccaagagaagaaaaagaagagaaactagaaacagttaaagtgtctaataatgctgaagaccccaaagatctcatgttaagtggagaaagggttttgcaaactgaaagatctgtagagagtagcagtatttcattggtacctggtactgattatggcactcaggaaagtatctcgttactggaagttagcactctagggaaggcaaaaacagaaccaaataaatgtgtgagtcagtgtgcagcatttgaaaaccccaagggactaattcatggttgttccaaagataatagaaatgacacagaaggctttaagtatccattgggacatgaagttaaccacagtcgggaaacaagcatagaaatggaagaaagtgaacttgatgctcagtatttgcagaatacattcaaggtttcaaagcgccagtcatttgctccgttttcaaatccaggaaatgcagaagaggaatgtgcaacattctctgcccactctgggtccttaaagaaacaaagtccaaaagtcacttttgaatgtgaacaaaaggaagaaaatcaaggaaagaatgagtctaatatcaagcctgtacagacagttaatatcactgcaggctttcctgtggttggtcagaaagataagccagttgataatgccaaatgtagtatcaaaggaggctctaggttttgtctatcatctcagttcagaggcaacgaaactggactcattactccaaataaacatggacttttacaaaacccatatcgtataccaccactttttcccatcaagtcatttgttaaaactaaatgtaagaaaaatctgctagaggaaaactttgaggaacattcaatgtcacctgaaagagaaatgggaaatgagaacattccaagtacagtgagcacaattagccgtaataacattagagaaaatgtttttaaagaagccagctcaagcaatattaatgaagtaggttccagtactaatgaagtgggctccagtattaatgaaataggttccagtgatgaaaacattcaagcagaactaggtagaaacagaaggcccaaattgaatgctatgcttagattaggggttttgcaacctgaggtctataaacaaagtcttcctggaagtaattgtaagcatcctgaaataaaaaagcaagaatatgaagaagtagttcagactgttaatacagatttctctccatatctgatttcagataacttagaacagcctatgggaagtagtcatgcatctcaggtttgttctgagacacctgatgacctgttagatgatggtgaaataaaggaagatactagttttgctgaaaatgacattaaggaaagttctgctgtttttagcaaaagcgtccagaaaggagagcttagcaggagtcctagccctttcacccatacacatttggctcagggttaccgaagaggggccaagaaattagagtcctcagaagagaacttatctagtgaggatgaagagcttccctgcttccaacacttgttatttggtaaagtaaacaatataccttctcagtctactaggcatagcaccgttgctaccgagtgtctgtctaagaacacagaggagaatttattatcattgaagaatagcttaaatgactgcagtaaccaggtaatattggcaaaggcatctcaggaacatcaccttagtgaggaaacaaaatgttctgctagcttgttttcttcacagtgcagtgaattggaagacttgactgcaaatacaaacacccaggatcctttcttgattggttcttccaaacaaatgaggcatcagtctgaaagccagggagttggtctgagtgacaaggaattggtttcagatgatgaagaaagaggaacgggcttggaagaaaataatcaagaagagcaaagcatggattcaaacttaggtgaagcagcatctgggtgtgagagtgaaacaagcgtctctgaagactgctcagggctatcctctcagagtgacattttaaccactcagcagagggataccatgcaacataacctgataaagctccagcaggaaatggctgaactagaagctgtgttagaacagcatgggagccagccttctaacagctacccttccatcataagtgactcttctgcccttgaggacctgcgaaatccagaacaaagcacatcagaaaaagcagtattaacttcacagaaaagtagtgaataccctataagccagaatccagaaggcctttctgctgacaagtttgaggtgtctgcagatagttctaccagtaaaaataaagaaccaggagtggaaaggtcatccccttctaaatgcccatcattagatgataggtggtacatgcacagttgctctgggagtcttcagaatagaaactacccatctcaagaggagctcattaaggttgttgatgtggaggagcaacagctggaagagtctgggccacacgatttgacggaaacatcttacttgccaaggcaagatctagagggaaccccttacctggaatctggaatcagcctcttctctgatgaccctgaatctgatccttctgaagacagagccccagagtcagctcgtgttggcaacataccatcttcaacctctgcattgaaagttccccaattgaaagttgcagaatctgcccagagtccagctgctgctcatactactgatactgctgggtataatgcaatggaagaaagtgtgagcagggagaagccagaattgacagcttcaacagaaagggtcaacaaaagaatgtccatggtggtgtctggcctgaccccagaagaatttatgctcgtgtacaagtttgccagaaaacaccacatcactttaactaatctaattactgaagagactactcatgttgttatgaaaacagatgctgagtttgtgtgtgaacggacactgaaatattttctaggaattgcgggaggaaaatgggtagttagctatttctgggtgacccagtctattaaagaaagaaaaatgctgaatgagcatgattttgaagtcagaggagatgtggtcaatggaagaaaccaccaaggtccaaagcgagcaagagaatcccaggacagaaagatcttcagggggctagaaatctgttgctatgggcccttcaccaacatgcccacagatcaactggaatggatggtacagctgtgtggtgcttctgtggtgaaggagctttcatcattcacccttggcacaggtgtccacccaattgtggttgtgcagccagatgcctggacagaggacaatggcttccatgcaattgggcagatgtgtgaggcacctgtggtgacccgagagtgggtgttggacagtgtagcactctaccagtgccaggagctggacacctacctgataccccagatcccccacagccactactga
>AF284812.BRCA1
catgattttgaagtcagaggagatgtggtcaatggaagaaaccaccaaggtccaaagcgagcaagagaatcccaggacagaaag
>AF507076.BRCA1
catgattttgaagtcagaggagatgtggtcaatggaagaaaccaccaaggtccaaagcgagcaagagaatcccaggacagaaag
-------------[p.65]---------------------------------------------------------------------------------------
> library(seqinr)
>
> choosebank("genbank")
>
>
> a1<-query(listname="actino", query="SP=Mycobacterium tuberculosis AND K=rpoB")
Warning message:
closing unused connection 4 (->pbil.univ-lyon1.fr:5558)
>
>
> a1<-query("actino", "SP=Mycobacterium tuberculosis AND K=rpoB")
>
> p1<-query("proteo", "SP=Escherichia coli AND K=rpoB")
>
> summary(a1$req)
Length Class Mode
[1,] 1 SeqAcnucWeb character
[2,] 1 SeqAcnucWeb character
[3,] 1 SeqAcnucWeb character
[4,] 1 SeqAcnucWeb character
[5,] 1 SeqAcnucWeb character
[6,] 1 SeqAcnucWeb character
[7,] 1 SeqAcnucWeb character
[8,] 1 SeqAcnuc
＜中略＞
[792,] 1 SeqAcnucWeb character
[793,] 1 SeqAcnucWeb character
[794,] 1 SeqAcnucWeb character
> summary(p1$req)
Length Class Mode
[1,] 1 SeqAcnucWeb character
[2,] 1 SeqAcnucWeb character
[3,] 1 SeqAcnucWeb character
[4,] 1 SeqAcnucWeb character
[5,] 1 SeqAcnucWeb character
[6,] 1 SeqAcnucWeb character
[7,] 1 SeqAcnucWeb character
[8,] 1 SeqAcnucWeb character
＜中略＞
[251,] 1 SeqAcnucWeb character
[252,] 1 SeqAcnucWeb character
> a1_seq644 <- getSequence(a1$req[[644]])
>
> p1_seq1 <- getSequence(p1$req[[1]])
>
>
> table(a1_seq644)
a1_seq644
a c g t
678 1086 1191 582
>
>
> table(p1_seq1)
p1_seq1
a c g t y
1013 1026 1090 899 1
----------------------------------------
＜宿題＞
次の塩基パターンの定義について調べてください。
r, y, w, s, k, m, d, h, n
(ex. y= C / T)
-----------------------------------------
>
> table(p1_seq1)/length(p1_seq1)
p1_seq1
a c g t y
0.2514271531 0.2546537602 0.2705385952 0.2231322909 0.0002482005
>
>
>
> table(mysequence) アミノ酸配列のケース
mysequence
a c d e f g h i k l m n p q r s t v
20 2 13 29 7 8 2 10 20 24 8 14 5 16 10 18 12 11
w y
2 12
>
-------------[p.67 10以降、GC含量の計算]-------------------------------------------------------------
> GC(a1_seq644)
[1] 0.6437659
>
> GC(p1_seq1)
[1] 0.5253227
>
>
>
> barplot(c(Actinobacteria=GC(a1_seq644),Proteobacteria=GC(p1_seq1)),col=heat.colors(2),ylim=c(0,1.0),ylab="GC-content")
>
>
>
> seqinr::count(a1_seq644,wordsize=2)
aa ac ag at ca cc cg ct ga gc gg gt ta tc tg tt
131 232 194 120 218 289 433 146 290 340 326 235 39 225 237 81
> seqinr::count(a1_seq644,wordsize=1)
a c g t
678 1086 1191 582
> seqinr::count(a1_seq644,wordsize=3)
aaa aac aag aat aca acc acg act aga agc agg agt ata
18 47 56 9 46 77 86 23 43 55 71 25 3
atc atg att caa cac cag cat cca ccc ccg cct cga cgc
65 40 12 70 59 41 48 61 60 135 33 133 111
cgg cgt cta ctc ctg ctt gaa gac gag gat gca gcc gcg
119 70 16 31 79 20 38 101 93 58 62 102 108
gct gga ggc ggg ggt gta gtc gtg gtt taa tac tag tat
68 65 102 64 95 18 85 92 40 5 25 4 5
tca tcc tcg tct tga tgc tgg tgt tta ttc ttg ttt
49 50 104 22 49 72 72 44 2 44 26 9
------------------------
> GC(p1_seq1)
[1] 0.5253227
>
> p1_tab<-table(p1_seq1)
> p1_tab
p1_seq1
a c g t y
1013 1026 1090 899 1
>
> myGC <- sum(p1_tab[2],p1_tab[3])/sum(p1_tab)
>
> myGC
[1] 0.5251924
>
> myGC_pct <- myGC*100
>
> myGC_pct
[1] 52.51924
>
