WABI ClustalW（休止中）
CLUSTALWのjobの投入
以下のパラメーターを POST します。
format, result は必須です。
result に mail を指定した場合は address も必須となります。
| パラメーター | 説明 |
|---|---|
| format | request ID を返す際の応答データの形式。 text, json, xml,bigfile, imagefile, requestfile が受け付けられますが、job投入時に意味があるのは text, json, xml の3つです。 |
| querySequence | multiple alignment 実行時、または系統樹作成時に clustalw に渡す配列ファイル。 NBRF-PIR, EMBL-SWISSPROT, Pearson (Fasta), Clustal (*.aln), GCG-MSF (Pileup), GCG9-RSF, GDE flat file の7フォーマットを使用できます。 |
| profile1 | profile alignment 実行時に clustalw に -PROFILE1= で 渡す整列済み配列ファイル。 |
| profile2 | profile alignment 実行時に clustalw に -PROFILE2= で渡す未整列の配列ファイルまたは整列済み配列ファイル。 |
| guidetree1 | multiple alignment 実行時に clustalw に -USETREE= で渡す、または profile alignment 実行時に clustalw に -USETREE1= で渡すガイドツリーファイル。 |
| guidetree2 | profile alignment 実行時に clustalw に -USETREE2= で渡すガイドツリーファイル。 |
| pwAaMatrix | pairwise alignment 実行時に clustalw に -PWMATRIX= で渡すカスタム weight matrix ファイル。 |
| pwDnaMatrix | pairwise alignment 実行時に clustalw に -PWDNAMATRIX= で渡すカスタム weight matrix ファイル。 |
| aaMatrix | multiple alignment 実行時に clustalw に -MATRIX= で渡すカスタム weight matrix ファイル。 |
| dnaMatrix | multiple alignment 実行時に clustalw に -DNAMATRIX= で渡すカスタム weight matrix ファイル。 |
| parameters | clustalw 実行時のコマンドラインオプションのうち、-INFILE=, -OUTFILE=, -NEWTREE=, -NEWTREE1=, -NEWTREE2=, -USETREE=, -USETREE1=, -USETREE2=, -STATS=, -OPTIONS, -HELP, -CHECK, -FULLHELP, -ALIGN, -INTERACTIVE 以外のものを記述します。 |
| result | 結果通知方法。 www, mailのいずれかが指定できます。 mail の場合、job 完了時に address に記述したメールアドレスに対して検索終了の通知が送信されます。 www の場合は何もしないので、POST 時に返された request ID を使って GET で job の状態を調べます。 |
| address | result で mail を指定した場合に検索終了の通知を受け取るメールアドレス。 |
CLUSTALWの結果の取得
| パラメーター | 説明 |
|---|---|
| GET clustalw/{id}?info=status | job が走っている、キューにたまっている、終わっている、存在しない、ということを返します。 |
| GET clustalw/{id}?info=request | プログラム実行条件を返します。 存在しない場合は、エラーを返します。 |
| GET clustalw/{id}?info=result | job が終わっていたら結果（multiple alignment, profile alignment を実行した場合は alignment の結果、-TREE を実行した場合は .ph ファイル、-BOOTSTRAP を実行した場合は .phb ファイル、-CONVERT を実行した場合はフォーマット変換後のファイル）を返します。 終わってない・存在しない場合は、エラーを返します。 |
| GET clustalw/{id}?info=result_guide1 | job が終わっていて -USETREE を指定しない multiple alignment または -SEQUENCES を指定して -USETREE を指定しないprofile alignment を実行した場合はガイドツリーファイルを、-USETREE1 を指定しない profile alignment を実行した場合はガイドツリーファイル1を返します。 終わっていない・存在しない場合はエラーを返す。 |
| GET clustalw/{id}?info=result_guide2 | job が終わっていて -USETREE2を 指定しない profile alignment を実行した場合はガイドツリーファイル2を返します。 終わっていない・存在しない場合はエラーを返す。 |
| GET clustalw/{id}?info=result_pim | job が終わっていて -TREE -PIM を実行した場合は percent identity matrix ファイルを返す。 終わっていない・存在しない場合はエラーを返す。 |
サンプルスクリプト
clustalw-client.pl
例1：複数配列のmultiple alignment
conf.json
{
"urlStr": "http://ddbj.nig.ac.jp/wabi/clustalw/",
"infile": "/home/hoge/cyc_aa.fasta",
"parameters": "-TYPE=PROTEIN -PWMATRIX=GONNET -PWGAPOPEN=10.00 -PWGAPEXT=0.10 -MATRIX=GONNET -GAPOPEN=10.00 -GAPEXT=0.20 -MAXDIV=30 -HGAPRESIDUES=GPSNDQEKR -GAPDIST=4 -ENDGAPS -OUTORDER=aligned",
"result": "www",
"address": ""
}
cyc_aa.fasta
>mms:mma_0447
MYRFTKTVVALLLATSGTMALAQAAYTNIGRPATAKEIAAWDIDVRPDFKGLPPGSGTVA
KGMAVWEGKCASCHGTFGESNEVFTPIVGGTTKEDIKSGHVAALSNNKQPQRTTIMKVPT
VSTLWDYINRAMPWTAPKSLTTEEVYAVTAYILNMAEILPDDFTLSDKNIAEVQQLMPNR
NGMTRNHGMWDIKGKPDVKSVACMKDCKTSTDLRSTLPEPSRNAHGNIQLQNRTFGEVRG
VDTTKPASTKPISAISADQKLAMATPAKPAAPAKVDGLALAKQYACVACHGVSNKIIGPG
FNEIAAKYKGDAAAPAALTAKIKNGSTGAWGPIPMPAQAHVKDEDIKTLVGWIIGGAK
>har:HEAR1189
MSRFTKTVVALALVATGAIACAQTAYPHIGRTATEKEIAAWDIDVRPDFKGLPKGSGTVS
KGMEVWEGKCASCHGTFGESNEVFTPIVGGTTKEDVKTGRVAALATNKQPQRTTMMKVAT
VSTLWDYINRAMPWTAPKSLTTEEVYAVTAYILNMSEVLPDDFTLSDKNIAEVQKLMPNR
NGMTQKHGMWDVKGKPDVKSVACMKDCQVSGDIRSSLPEPSRNAHGNIQEQNRSFGEVRG
VNTTVPASTTPISSATRKSVVATAATTAPAEAAAKPKALGLAKQYACIACHGVSNKIVGP
GFNEIAAKYKGDSAAATTLFDKVKNGSSGAWGPVPMPGQAHVKDEDVKTLVSWILSGAK
>pnu:Pnuc_0802
MFKLAKVAKFTLFAVTTFFAVGSVVAQNSSTHYPGIGRDATPAEVAAWDIDVRPDFKGLP
KGSGSVEKGQQLWEAKCSVCHGTFGESNEIFTPIIGGTTTDDIKTGRVASLSDRKQPQRT
TIMKVATVSSLWDYIYRAMPWNAPRSLTPDDTFALVAYLLNMAEVVPDDFVLSNTNIAEV
QKRMPNRNGMTLKHGLWNSKGTPDVHATACMTNCVQFVQIGSELPDYARNAHGNIAEQNR
QYGPFRGSDSTKPPLTKLPGASAEGLAHASETHASKKGPAELFKSENCTACHAMSTKLVG
PSVADIAAKYQGQSGALDTLMAKVKNGGSGVWGPIPMPAQSQLSDEDRKALVTWVLSGGK
>bprc:D521_0984
MFKLDKFSISLGFAALIAITAQAALAQSGSAKFPGIGRAATPAEVAAWDIDVRPDFKGLP
KGSGSVEKGQVIWEAKCASCHGTFGESNEIFTPIAGGTTKDDVKTGRVASLKDMKQPQRT
TLMKVPTVSTLWDYIYRAMPWNAPRSLTPDDTYALVAFILSLGEIVPDDFVLSDKNIAEV
KMPNRNGMTTKHGFWSVSGKPDVNGNACMHNCVPFVQIGSTLPDFARNAHENIAEQNRMY
GPYRGADTSKPPIKQLPGASGEGLAHAADTHTSAAKGPAALFKNENCSACHAPNAKLVGP
SIADIAKKYEGQSGAVDRLMAKVKNGGAGVWGSIPMPPQAQLSDDDRKTLVVWMLSGGK
>dar:Daro_3133
MSRFSKTILVLALLGASSTGFSFENFKGVGRQATPAEVKAWDIDVRPDFKGLPKGKGNVE
RGNELFEEKCASCHGSFGESNEVFTPLAGGTTKDDIKTGRVKGLSSGELPQRTTFTKVAT
ISTVFDYIQRAMPWTAPKSLKPDDVYAILAYLLNLQEIVPADFELSDRNIADVQKLLPNR
NGMTTDHGLWPGASAKKGGIGNGGIPDVKNVACMKNCKPEVQIGSTLPEYARTAHGELAD
QNRNFGAVRGTRTLGPEAAKKAADAGTLELATKSGCMACHGMKSKIVGPGYSEVVARYQG
QPDAESRLIAKVKAGGQGVWGSIPMPPNAHVKDEDLKTLVQWILAGSK
multi fasta データから pairewise alignment、ガイドツリー生成、multiple alignment
を行う場合のサンプル
（conf.json に記述したパラメータ値は clustalw2 のデフォルト値であるので、parameters
に何も指定しない場合と同一の結果が得られます。）
$ perl clustalw-client.pl conf.json
Execute multiple sequence alignment.
request-ID: wabi_clustalw_2013-0827-1814-55-821-640340
waiting
finished
ClustalW2 result is outputed to wabi_clustalw_2013-0827-1814-55-821-640340.txt
Guide Tree 1 is outputed to wabi_clustalw_2013-0827-1814-55-821-640340_guidetree1.txt
$ cat wabi_clustalw_2013-0827-1814-55-821-640340.txt
CLUSTAL 2.1 multiple sequence alignment
mms_mma_0447 MYRFTKTVVALLLAT-------SGTMALAQAAYTNIGRPATAKEIAAWDIDVRPDFKGLP
har_HEAR1189 MSRFTKTVVALALVA-------TGAIACAQTAYPHIGRTATEKEIAAWDIDVRPDFKGLP
dar_Daro_3133 MSRFSKTILVLALLG-------ASSTGFSFENFKGVGRQATPAEVKAWDIDVRPDFKGLP
pnu_Pnuc_0802 MFKLAKVAKFTLFAVTTFFAVGSVVAQNSSTHYPGIGRDATPAEVAAWDIDVRPDFKGLP
bprc_D521_0984 MFKLDKFSISLGFAALIAITAQAALAQSGSAKFPGIGRAATPAEVAAWDIDVRPDFKGLP
* :: * : : . : :** ** *: **************
mms_mma_0447 PGSGTVAKGMAVWEGKCASCHGTFGESNEVFTPIVGGTTKEDIKSGHVAALSNNKQPQRT
har_HEAR1189 KGSGTVSKGMEVWEGKCASCHGTFGESNEVFTPIVGGTTKEDVKTGRVAALATNKQPQRT
dar_Daro_3133 KGKGNVERGNELFEEKCASCHGSFGESNEVFTPLAGGTTKDDIKTGRVKGLSSGELPQRT
pnu_Pnuc_0802 KGSGSVEKGQQLWEAKCSVCHGTFGESNEIFTPIIGGTTTDDIKTGRVASLSDRKQPQRT
bprc_D521_0984 KGSGSVEKGQVIWEAKCASCHGTFGESNEIFTPIAGGTTKDDVKTGRVASLKDMKQPQRT
*.*.* :* ::* **: ***:******:***: ****.:*:*:*:* .* : ****
mms_mma_0447 TIMKVPTVSTLWDYINRAMPWTAPKSLTTEEVYAVTAYILNMAEILPDDFTLSDKNIAEV
har_HEAR1189 TMMKVATVSTLWDYINRAMPWTAPKSLTTEEVYAVTAYILNMSEVLPDDFTLSDKNIAEV
dar_Daro_3133 TFTKVATISTVFDYIQRAMPWTAPKSLKPDDVYAILAYLLNLQEIVPADFELSDRNIADV
pnu_Pnuc_0802 TIMKVATVSSLWDYIYRAMPWNAPRSLTPDDTFALVAYLLNMAEVVPDDFVLSNTNIAEV
bprc_D521_0984 TLMKVPTVSTLWDYIYRAMPWNAPRSLTPDDTYALVAFILSLGEIVPDDFVLSDKNIAEV
*: **.*:*:::*** *****.**:**..::.:*: *::*.: *::* ** **: ***:*
mms_mma_0447 QQLMPNRNGMTRNHGMWD---IK-------GKPDVKSVACMKDCKTSTDLRSTLPEPSRN
har_HEAR1189 QKLMPNRNGMTQKHGMWD---VK-------GKPDVKSVACMKDCQVSGDIRSSLPEPSRN
dar_Daro_3133 QKLLPNRNGMTTDHGLWPGASAKKGGIGNGGIPDVKNVACMKNCKPEVQIGSTLPEYART
pnu_Pnuc_0802 QKRMPNRNGMTLKHGLWN---SK-------GTPDVHATACMTNCVQFVQIGSELPDYARN
bprc_D521_0984 K--MPNRNGMTTKHGFWS---VS-------GKPDVNGNACMHNCVPFVQIGSTLPDFARN
: :******* .**:* . * ***: *** :* :: * **: :*.
mms_mma_0447 AHGNIQLQNRTFGEVRGVDTTKPASTKPISAISADQKLA-MATPAKPAAPAKVDGLALAK
har_HEAR1189 AHGNIQEQNRSFGEVRGVNTTVPASTTPISSATRKSVVATAATTAPAEAAAKPKALGLAK
dar_Daro_3133 AHGELADQNRNFGAVRGTRTLGPEAAK---------------------KAADAGTLELAT
pnu_Pnuc_0802 AHGNIAEQNRQYGPFRGSDSTKPPLTKLPGASAEG-----LAHASETHASK-KGPAELFK
bprc_D521_0984 AHENIAEQNRMYGPYRGADTSKPPIKQLPGASGEG-----LAHAADTHTSAAKGPAALFK
** :: *** :* ** : * . * .
mms_mma_0447 QYACVACHGVSNKIIGPGFNEIAAKYKGDAAAPAALTAKIKNGSTGAWGPIPMPAQAHVK
har_HEAR1189 QYACIACHGVSNKIVGPGFNEIAAKYKGDSAAATTLFDKVKNGSSGAWGPVPMPGQAHVK
dar_Daro_3133 KSGCMACHGMKSKIVGPGYSEVVARYQGQPDAESRLIAKVKAGGQGVWGSIPMPPNAHVK
pnu_Pnuc_0802 SENCTACHAMSTKLVGPSVADIAAKYQGQSGALDTLMAKVKNGGSGVWGPIPMPAQSQLS
bprc_D521_0984 NENCSACHAPNAKLVGPSIADIAKKYEGQSGAVDRLMAKVKNGGAGVWGSIPMPPQAQLS
. * ***. . *::**. ::. :*:*:. * * *:* *. *.**.:*** ::::.
mms_mma_0447 DEDIKTLVGWIIGGAK
har_HEAR1189 DEDVKTLVSWILSGAK
dar_Daro_3133 DEDLKTLVQWILAGSK
pnu_Pnuc_0802 DEDRKALVTWVLSGGK
bprc_D521_0984 DDDRKTLVVWMLSGGK
*:* *:** *::.*.*
例2：ガイドツリーを使ったmultiple alignmentの再実行
conf.json
{
"urlStr": "http://ddbj.nig.ac.jp/wabi/clustalw/",
"infile": "/home/hoge/cyc_aa.fasta",
"guidetree1": "/home/hoge/wabi_clustalw_2013-0827-1814-55-821-640340_guidetree1.txt",
"parameters": "-TYPE=PROTEIN -MATRIX=GONNET -GAPOPEN=12.00 -GAPEXT=0.40 -MAXDIV=30 -HGAPRESIDUES=GPSNDQEKR -GAPDIST=4 -ENDGAPS",
"result": "www",
"address": ""
}
例1で生成されたガイドツリー（wabi_clustalw_2013-0827-1814-55-821-640340_guidetree1.txt）を使い、multiple alignment のみをパラメータを変えて再実行する場合のサンプル
$ perl clustalw-client.pl conf.json
Execute multiple sequence alignment.
request-ID: wabi_clustalw_2013-0828-1125-32-853-013077
waiting
finished
ClustalW2 result is outputed to wabi_clustalw_2013-0828-1125-32-853-013077.txt
$ cat wabi_clustalw_2013-0828-1125-32-853-013077.txt
CLUSTAL 2.1 multiple sequence alignment
mms_mma_0447 MYRFTKTVVALLLAT-------SGTMALAQAAYTNIGRPATAKEIAAWDIDVRPDFKGLP
har_HEAR1189 MSRFTKTVVALALVA-------TGAIACAQTAYPHIGRTATEKEIAAWDIDVRPDFKGLP
dar_Daro_3133 MSRFSKTILVLALLG-------ASSTGFSFENFKGVGRQATPAEVKAWDIDVRPDFKGLP
pnu_Pnuc_0802 MFKLAKVAKFTLFAVTTFFAVGSVVAQNSSTHYPGIGRDATPAEVAAWDIDVRPDFKGLP
bprc_D521_0984 MFKLDKFSISLGFAALIAITAQAALAQSGSAKFPGIGRAATPAEVAAWDIDVRPDFKGLP
* :: * : : . : :** ** *: **************
mms_mma_0447 PGSGTVAKGMAVWEGKCASCHGTFGESNEVFTPIVGGTTKEDIKSGHVAALSNNKQPQRT
har_HEAR1189 KGSGTVSKGMEVWEGKCASCHGTFGESNEVFTPIVGGTTKEDVKTGRVAALATNKQPQRT
dar_Daro_3133 KGKGNVERGNELFEEKCASCHGSFGESNEVFTPLAGGTTKDDIKTGRVKGLSSGELPQRT
pnu_Pnuc_0802 KGSGSVEKGQQLWEAKCSVCHGTFGESNEIFTPIIGGTTTDDIKTGRVASLSDRKQPQRT
bprc_D521_0984 KGSGSVEKGQVIWEAKCASCHGTFGESNEIFTPIAGGTTKDDVKTGRVASLKDMKQPQRT
*.*.* :* ::* **: ***:******:***: ****.:*:*:*:* .* : ****
mms_mma_0447 TIMKVPTVSTLWDYINRAMPWTAPKSLTTEEVYAVTAYILNMAEILPDDFTLSDKNIAEV
har_HEAR1189 TMMKVATVSTLWDYINRAMPWTAPKSLTTEEVYAVTAYILNMSEVLPDDFTLSDKNIAEV
dar_Daro_3133 TFTKVATISTVFDYIQRAMPWTAPKSLKPDDVYAILAYLLNLQEIVPADFELSDRNIADV
pnu_Pnuc_0802 TIMKVATVSSLWDYIYRAMPWNAPRSLTPDDTFALVAYLLNMAEVVPDDFVLSNTNIAEV
bprc_D521_0984 TLMKVPTVSTLWDYIYRAMPWNAPRSLTPDDTYALVAFILSLGEIVPDDFVLSDKNIAEV
*: **.*:*:::*** *****.**:**..::.:*: *::*.: *::* ** **: ***:*
mms_mma_0447 QQLMPNRNGMTRNHGMWDIK----------GKPDVKSVACMKDCKTSTDLRSTLPEPSRN
har_HEAR1189 QKLMPNRNGMTQKHGMWDVK----------GKPDVKSVACMKDCQVSGDIRSSLPEPSRN
dar_Daro_3133 QKLLPNRNGMTTDHGLWPGASAKKGGIGNGGIPDVKNVACMKNCKPEVQIGSTLPEYART
pnu_Pnuc_0802 QKRMPNRNGMTLKHGLWNSK----------GTPDVHATACMTNCVQFVQIGSELPDYARN
bprc_D521_0984 K--MPNRNGMTTKHGFWSVS----------GKPDVNGNACMHNCVPFVQIGSTLPDFARN
: :******* .**:* * ***: *** :* :: * **: :*.
mms_mma_0447 AHGNIQLQNRTFGEVRGVDTTKPASTKPISAISADQKLAMATPAKPAAP-AKVDGLALAK
har_HEAR1189 AHGNIQEQNRSFGEVRGVNTTVPASTTPISSATRKSVVATAATTAPAEAAAKPKALGLAK
dar_Daro_3133 AHGELADQNRNFGAVRGTRTLGPEAAKKAADAG---------------------TLELAT
pnu_Pnuc_0802 AHGNIAEQNRQYGPFRGSDSTKPPLTKLPGASAEGLAHASETHASK------KGPAELFK
bprc_D521_0984 AHENIAEQNRMYGPYRGADTSKPPIKQLPGASGEGLAHAADTHTSAA-----KGPAALFK
** :: *** :* ** : * . * .
mms_mma_0447 QYACVACHGVSNKIIGPGFNEIAAKYKGDAAAPAALTAKIKNGSTGAWGPIPMPAQAHVK
har_HEAR1189 QYACIACHGVSNKIVGPGFNEIAAKYKGDSAAATTLFDKVKNGSSGAWGPVPMPGQAHVK
dar_Daro_3133 KSGCMACHGMKSKIVGPGYSEVVARYQGQPDAESRLIAKVKAGGQGVWGSIPMPPNAHVK
pnu_Pnuc_0802 SENCTACHAMSTKLVGPSVADIAAKYQGQSGALDTLMAKVKNGGSGVWGPIPMPAQSQLS
bprc_D521_0984 NENCSACHAPNAKLVGPSIADIAKKYEGQSGAVDRLMAKVKNGGAGVWGSIPMPPQAQLS
. * ***. . *::**. ::. :*:*:. * * *:* *. *.**.:*** ::::.
mms_mma_0447 DEDIKTLVGWIIGGAK
har_HEAR1189 DEDVKTLVSWILSGAK
dar_Daro_3133 DEDLKTLVQWILAGSK
pnu_Pnuc_0802 DEDRKALVTWVLSGGK
bprc_D521_0984 DDDRKTLVVWMLSGGK
*:* *:** *::.*.*
同じ処理をコマンドラインで実行する場合
$ clustalw2 -INFILE=cyc_aa.fasta -USETREE=wabi_clustalw_2013-0827-1814-55-821-640340_guidetree1.txt -TYPE=PROTEIN \
> -MATRIX=GONNET -GAPOPEN=12.00 -GAPEXT=0.40 -MAXDIV=30 -HGAPRESIDUES=GPSNDQEKR -GAPDIST=4 -ENDGAPS
例3：整列済みデータへの新規配列の追加（profile alignment）
cyc_aa2.fasta
>lch:Lcho_3783
MSSSPKWLAAAVLALAAAGSLAQVTAVGIGRAATEKEIKAWDIDVRPDFKGLPKGSGTVE
QGMEVWEAKCAHCHGVFGESNEVFSPLVGGTTADDVKTGHVARLNDPTFPGRTTLMKVAT
VSTLWDYINRAMPWTAPKSLKTDEVYAVTAYLLNMGDVLPAGFVLSDQTIAQAQARMPNR
NGMTLDHGMWPGRGLKTAAKPDVKVAACMSNCEAEPKVASFLPDFARNAHGNLAEQTRMV
GAQHGVDTTRPPGAAPTLAAAPVVAKATDEGAAALALAAKHTCTACHAVDAKLVGPAFRE
IGKKHGSRADAVAYLTGKIKSGGTGVWGAIPMPAQTLPDADAKLIANWLAAGAKK
>reh:H16_A3571
MSMWAELRTAAALVLAAVSAAPAWAGTADARAALGRTATPAEVAAWDIDVRPDFQGLPRG
SGTVAQGQKVWDGKCASCHGDFGESNEVFTPLVGGTTAEDIRRGRVAGMTGNQPYRTTLM
KVSTVSTLWDYIHRAMPWNAPKSLSVGDVYAVTAYMLHLGEVVPADFTLSDANIAEIQRR
MPNRDGMTTGHGLWPGRGRPDTRNTACMKDCAGKVAITSSIPDYARDAHGELAQQQRSFG
PVRGVAAGNTVSKSAASAPSEPAAPGARLTSQYQCMACHAMDRKLVGPSFADIAGKYKGQ
DAHGALARKVKAGGQGAWGSVPMPAQPQIPDSDVQAMVGWILEAK
conf.json
{
"urlStr": "http://ddbj.nig.ac.jp/wabi/clustalw/",
"profile1": "/home/hoge/wabi_clustalw_2013-0827-1814-55-821-640340.txt",
"profile2": "/home/hoge/cyc_aa2.fasta",
"parameters": "-SEQUENCES -TYPE=PROTEIN -MATRIX=GONNET -GAPOPEN=10.00 -GAPEXT=0.20 -MAXDIV=30 -HGAPRESIDUES=GPSNDQEKR -GAPDIST=4 -ENDGAPS",
"result": "www",
"address": ""
}
例1の整列結果（wabi_clustalw_2013-0827-1814-55-821-640340.txt）に、新たな配列（cyc_aa2.fasta）を追加する場合のサンプル
$ perl clustalw-client.pl conf.json
Execute multiple sequence alignment.
request-ID: wabi_clustalw_2013-0828-1452-47-561-627715
waiting
finished
ClustalW2 result is outputed to wabi_clustalw_2013-0828-1452-47-561-627715.txt
Guide Tree 2 is outputed to wabi_clustalw_2013-0828-1452-47-561-627715_guidetree1.txt
$ cat wabi_clustalw_2013-0828-1452-47-561-627715.txt
CLUSTAL 2.1 multiple sequence alignment
mms_mma_0447 --MYRFTKTVVALLLAT-------SGTMALAQAAYTNIGRPATAKEIAAWDIDVRPDFKG
har_HEAR1189 --MSRFTKTVVALALVA-------TGAIACAQTAYPHIGRTATEKEIAAWDIDVRPDFKG
dar_Daro_3133 --MSRFSKTILVLALLG-------ASSTGFSFENFKGVGRQATPAEVKAWDIDVRPDFKG
pnu_Pnuc_0802 --MFKLAKVAKFTLFAVTTFFAVGSVVAQNSSTHYPGIGRDATPAEVAAWDIDVRPDFKG
bprc_D521_0984 --MFKLDKFSISLGFAALIAITAQAALAQSGSAKFPGIGRAATPAEVAAWDIDVRPDFKG
lch_Lcho_3783 --MSSSPKWLAAAVLAL-------AAAGSLAQVTAVGIGRAATEKEIKAWDIDVRPDFKG
reh_H16_A3571 MSMWAELRTAAALVLAAVS----AAPAWAGTADARAALGRTATPAEVAAWDIDVRPDFQG
* : : : :** ** *: **********:*
mms_mma_0447 LPPGSGTVAKGMAVWEGKCASCHGTFGESNEVFTPIVGGTTKEDIKSGHVAALSNNKQPQ
har_HEAR1189 LPKGSGTVSKGMEVWEGKCASCHGTFGESNEVFTPIVGGTTKEDVKTGRVAALATNKQPQ
dar_Daro_3133 LPKGKGNVERGNELFEEKCASCHGSFGESNEVFTPLAGGTTKDDIKTGRVKGLSSGELPQ
pnu_Pnuc_0802 LPKGSGSVEKGQQLWEAKCSVCHGTFGESNEIFTPIIGGTTTDDIKTGRVASLSDRKQPQ
bprc_D521_0984 LPKGSGSVEKGQVIWEAKCASCHGTFGESNEIFTPIAGGTTKDDVKTGRVASLKDMKQPQ
lch_Lcho_3783 LPKGSGTVEQGMEVWEAKCAHCHGVFGESNEVFSPLVGGTTADDVKTGHVARLNDPTFPG
reh_H16_A3571 LPRGSGTVAQGQKVWDGKCASCHGDFGESNEVFTPLVGGTTAEDIRRGRVAGMTGN-QPY
** *.*.* :* ::: **: *** ******:*:*: **** :*:: *:* : *
mms_mma_0447 RTTIMKVPTVSTLWDYINRAMPWTAPKSLTTEEVYAVTAYILNMAEILPDDFTLSDKNIA
har_HEAR1189 RTTMMKVATVSTLWDYINRAMPWTAPKSLTTEEVYAVTAYILNMSEVLPDDFTLSDKNIA
dar_Daro_3133 RTTFTKVATISTVFDYIQRAMPWTAPKSLKPDDVYAILAYLLNLQEIVPADFELSDRNIA
pnu_Pnuc_0802 RTTIMKVATVSSLWDYIYRAMPWNAPRSLTPDDTFALVAYLLNMAEVVPDDFVLSNTNIA
bprc_D521_0984 RTTLMKVPTVSTLWDYIYRAMPWNAPRSLTPDDTYALVAFILSLGEIVPDDFVLSDKNIA
lch_Lcho_3783 RTTLMKVATVSTLWDYINRAMPWTAPKSLKTDEVYAVTAYLLNMGDVLPAGFVLSDQTIA
reh_H16_A3571 RTTLMKVSTVSTLWDYIHRAMPWNAPKSLSVGDVYAVTAYMLHLGEVVPADFTLSDANIA
***: **.*:*:::*** *****.**:**. :.:*: *::* : :::* .* **: .**
mms_mma_0447 EVQQLMPNRNGMTRNHGMWD---IK-------GKPDVKSVACMKDCKTSTDLRSTLPEPS
har_HEAR1189 EVQKLMPNRNGMTQKHGMWD---VK-------GKPDVKSVACMKDCQVSGDIRSSLPEPS
dar_Daro_3133 DVQKLLPNRNGMTTDHGLWPGASAKKGGIGNGGIPDVKNVACMKNCKPEVQIGSTLPEYA
pnu_Pnuc_0802 EVQKRMPNRNGMTLKHGLWN---SK-------GTPDVHATACMTNCVQFVQIGSELPDYA
bprc_D521_0984 EVK--MPNRNGMTTKHGFWS---VS-------GKPDVNGNACMHNCVPFVQIGSTLPDFA
lch_Lcho_3783 QAQARMPNRNGMTLDHGMWPGRGLKT-----AAKPDVKVAACMSNCEAEPKVASFLPDFA
reh_H16_A3571 EIQRRMPNRDGMTTGHGLWP---GR-------GRPDTRNTACMKDCAGKVAITSSIPDYA
: : :***:*** **:* . **.. *** :* : * :*: :
mms_mma_0447 RNAHGNIQLQNRTFGEVRGVDTTKPASTKPISAISADQKLA-MATPAKPAAPAKVDGLAL
har_HEAR1189 RNAHGNIQEQNRSFGEVRGVNTTVPASTTPISSATRKSVVATAATTAPAEAAAKPKALGL
dar_Daro_3133 RTAHGELADQNRNFGAVRGTRTLGPEAAK---------------------KAADAGTLEL
pnu_Pnuc_0802 RNAHGNIAEQNRQYGPFRGSDSTKPPLTKLPGASAEG-----LAHASETHASK-KGPAEL
bprc_D521_0984 RNAHENIAEQNRMYGPYRGADTSKPPIKQLPGASGEG-----LAHAADTHTSAAKGPAAL
lch_Lcho_3783 RNAHGNLAEQTRMVGAQHGVDTTRPPGAAPTLAAAP---------VVAKATDEGAAALAL
reh_H16_A3571 RDAHGELAQQQRSFGPVRGVAAGNTVSKS----------------AASAPSEPAAPGARL
* ** :: * * * :* : . *
mms_mma_0447 AKQYACVACHGVSNKIIGPGFNEIAAKYKGDAAAPAALTAKIKNGSTGAWGPIPMPAQAH
har_HEAR1189 AKQYACIACHGVSNKIVGPGFNEIAAKYKGDSAAATTLFDKVKNGSSGAWGPVPMPGQAH
dar_Daro_3133 ATKSGCMACHGMKSKIVGPGYSEVVARYQGQPDAESRLIAKVKAGGQGVWGSIPMPPNAH
pnu_Pnuc_0802 FKSENCTACHAMSTKLVGPSVADIAAKYQGQSGALDTLMAKVKNGGSGVWGPIPMPAQSQ
bprc_D521_0984 FKNENCSACHAPNAKLVGPSIADIAKKYEGQSGAVDRLMAKVKNGGAGVWGSIPMPPQAQ
lch_Lcho_3783 AAKHTCTACHAVDAKLVGPAFREIGKKHGSRADAVAYLTGKIKSGGTGVWGAIPMPAQT-
reh_H16_A3571 TSQYQCMACHAMDRKLVGPSFADIAGKYKGQ-DAHGALARKVKAGGQGAWGSVPMPAQPQ
. * ***. . *::**. :: :: . * * *:* *. *.**.:*** :.
mms_mma_0447 VKDEDIKTLVGWIIGGAK-
har_HEAR1189 VKDEDVKTLVSWILSGAK-
dar_Daro_3133 VKDEDLKTLVQWILAGSK-
pnu_Pnuc_0802 LSDEDRKALVTWVLSGGK-
bprc_D521_0984 LSDDDRKTLVVWMLSGGK-
lch_Lcho_3783 LPDADAKLIANWLAAGAKK
reh_H16_A3571 IPDSDVQAMVGWILEAK--
: * * : :. *: .
同じ処理をコマンドラインで実行する場合
$ clustalw2 -PROFILE1=wabi_clustalw_2013-0827-1814-55-821-640340.txt -PROFILE2=cyc_aa2.fasta -SEQUENCES -TYPE=PROTEIN \
> -MATRIX=GONNET -GAPOPEN=10.00 -GAPEXT=0.20 -MAXDIV=30 -HGAPRESIDUES=GPSNDQEKR -GAPDIST=4 -ENDGAPS
例4：2つの整列済みデータの統合（profile alignment）
conf.json
{
"urlStr": "http://ddbj.nig.ac.jp/wabi/clustalw/",
"profile1": "/home/hoge/wabi_clustalw_2013-0827-1814-55-821-640340.txt",
"profile2": "/home/hoge/cyc_aa2.aln",
"parameters": "-PROFILE -TYPE=PROTEIN -MATRIX=GONNET -GAPOPEN=10.00 -GAPEXT=0.20 -MAXDIV=30 -HGAPRESIDUES=GPSNDQEKR -GAPDIST=4 -ENDGAPS",
"result": "www",
"address": ""
}
cyc_aa2.aln
CLUSTAL 2.1 multiple sequence alignment
lch_Lcho_3783 MSSSPKWLAAAVLALAAAGSLAQVTAVG-----IGRAATEKEIKAWDIDVRPDFKGLPKG
reh_H16_A3571 MSMWAELRTAAALVLAAVSAAPAWAGTADARAALGRTATPAEVAAWDIDVRPDFQGLPRG
** .: :**.*.***..: . :... :**:** *: **********:***:*
lch_Lcho_3783 SGTVEQGMEVWEAKCAHCHGVFGESNEVFSPLVGGTTADDVKTGHVARLNDPTFPGRTTL
reh_H16_A3571 SGTVAQGQKVWDGKCASCHGDFGESNEVFTPLVGGTTAEDIRRGRVAGMTG-NQPYRTTL
**** ** :**:.*** *** ********:********:*:: *:** :.. . * ****
lch_Lcho_3783 MKVATVSTLWDYINRAMPWTAPKSLKTDEVYAVTAYLLNMGDVLPAGFVLSDQTIAQAQA
reh_H16_A3571 MKVSTVSTLWDYIHRAMPWNAPKSLSVGDVYAVTAYMLHLGEVVPADFTLSDANIAEIQR
***:*********:*****.*****...:*******:*::*:*:**.*.*** .**: *
lch_Lcho_3783 RMPNRNGMTLDHGMWPGRGLKTAAKPDVKVAACMSNCEAEPKVASFLPDFARNAHGNLAE
reh_H16_A3571 RMPNRDGMTTGHGLWPGRG-----RPDTRNTACMKDCAGKVAITSSIPDYARDAHGELAQ
*****:*** .**:***** :**.: :***.:* .: ::* :**:**:***:**:
lch_Lcho_3783 QTRMVGAQHGVDTTRPPGAAPTLAAAPVVAKATDEGAAALALAAKHTCTACHAVDAKLVG
reh_H16_A3571 QQRSFGPVRGVAAGN--TVSKSAASAP-----SEPAAPGARLTSQYQCMACHAMDRKLVG
* * .*. :** : . .: : *:** :: .*.. *:::: * ****:* ****
lch_Lcho_3783 PAFREIGKKHGSRADAVAYLTGKIKSGGTGVWGAIPMPAQ-TLPDADAKLIANWLAAGAK
reh_H16_A3571 PSFADIAGKYKG-QDAHGALARKVKAGGQGAWGSVPMPAQPQIPDSDVQAMVGWILEAK-
*:* :*. *: . ** . *: *:*:** *.**::***** :**:*.: :..*: .
lch_Lcho_3783 K
reh_H16_A3571 -
例3の cyc_aa2.fasta の multiple alignment 結果（cyc_aa2.aln）と例1の multiple alignment 結果（wabi_clustalw_2013-0827-1814-55-821-640340.txt）を統合する場合のサンプル
$ perl clustalw-client3.pl conf.json
Execute multiple sequence alignment.
request-ID: wabi_clustalw_2013-0829-1608-33-594-650129
waiting
waiting
finished
ClustalW2 result is outputed to wabi_clustalw_2013-0829-1608-33-594-650129.txt
Guide Tree 1 is outputed to wabi_clustalw_2013-0829-1608-33-594-650129_guidetree1.txt
Guide Tree 2 is outputed to wabi_clustalw_2013-0829-1608-33-594-650129_guidetree1.txt
$ cat wabi_clustalw_2013-0829-1608-33-594-650129.txt
CLUSTAL 2.1 multiple sequence alignment
mms_mma_0447 MYRFTKTVVALLLAT-------SGTMALAQAAYTN-----IGRPATAKEIAAWDIDVRPD
har_HEAR1189 MSRFTKTVVALALVA-------TGAIACAQTAYPH-----IGRTATEKEIAAWDIDVRPD
dar_Daro_3133 MSRFSKTILVLALLG-------ASSTGFSFENFKG-----VGRQATPAEVKAWDIDVRPD
pnu_Pnuc_0802 MFKLAKVAKFTLFAVTTFFAVGSVVAQNSSTHYPG-----IGRDATPAEVAAWDIDVRPD
bprc_D521_0984 MFKLDKFSISLGFAALIAITAQAALAQSGSAKFPG-----IGRAATPAEVAAWDIDVRPD
lch_Lcho_3783 MSSSPKWLAAAVLAL-------AAAGSLAQVTAVG-----IGRAATEKEIKAWDIDVRPD
reh_H16_A3571 MSMWAELRTAAALVL-------AAVSAAPAWAGTADARAALGRTATPAEVAAWDIDVRPD
* : : : :** ** *: *********
mms_mma_0447 FKGLPPGSGTVAKGMAVWEGKCASCHGTFGESNEVFTPIVGGTTKEDIKSGHVAALSNNK
har_HEAR1189 FKGLPKGSGTVSKGMEVWEGKCASCHGTFGESNEVFTPIVGGTTKEDVKTGRVAALATNK
dar_Daro_3133 FKGLPKGKGNVERGNELFEEKCASCHGSFGESNEVFTPLAGGTTKDDIKTGRVKGLSSGE
pnu_Pnuc_0802 FKGLPKGSGSVEKGQQLWEAKCSVCHGTFGESNEIFTPIIGGTTTDDIKTGRVASLSDRK
bprc_D521_0984 FKGLPKGSGSVEKGQVIWEAKCASCHGTFGESNEIFTPIAGGTTKDDVKTGRVASLKDMK
lch_Lcho_3783 FKGLPKGSGTVEQGMEVWEAKCAHCHGVFGESNEVFSPLVGGTTADDVKTGHVARLNDPT
reh_H16_A3571 FQGLPRGSGTVAQGQKVWDGKCASCHGDFGESNEVFTPLVGGTTAEDIRRGRVAGMTG-N
*:*** *.*.* :* ::: **: *** ******:*:*: **** :*:: *:* :
mms_mma_0447 QPQRTTIMKVPTVSTLWDYINRAMPWTAPKSLTTEEVYAVTAYILNMAEILPDDFTLSDK
har_HEAR1189 QPQRTTMMKVATVSTLWDYINRAMPWTAPKSLTTEEVYAVTAYILNMSEVLPDDFTLSDK
dar_Daro_3133 LPQRTTFTKVATISTVFDYIQRAMPWTAPKSLKPDDVYAILAYLLNLQEIVPADFELSDR
pnu_Pnuc_0802 QPQRTTIMKVATVSSLWDYIYRAMPWNAPRSLTPDDTFALVAYLLNMAEVVPDDFVLSNT
bprc_D521_0984 QPQRTTLMKVPTVSTLWDYIYRAMPWNAPRSLTPDDTYALVAFILSLGEIVPDDFVLSDK
lch_Lcho_3783 FPGRTTLMKVATVSTLWDYINRAMPWTAPKSLKTDEVYAVTAYLLNMGDVLPAGFVLSDQ
reh_H16_A3571 QPYRTTLMKVSTVSTLWDYIHRAMPWNAPKSLSVGDVYAVTAYMLHLGEVVPADFTLSDA
* ***: **.*:*:::*** *****.**:**. :.:*: *::* : :::* .* **:
mms_mma_0447 NIAEVQQLMPNRNGMTRNHGMWD---IK-------GKPDVKSVACMKDCKTSTDLRSTLP
har_HEAR1189 NIAEVQKLMPNRNGMTQKHGMWD---VK-------GKPDVKSVACMKDCQVSGDIRSSLP
dar_Daro_3133 NIADVQKLLPNRNGMTTDHGLWPGASAKKGGIGNGGIPDVKNVACMKNCKPEVQIGSTLP
pnu_Pnuc_0802 NIAEVQKRMPNRNGMTLKHGLWN---SK-------GTPDVHATACMTNCVQFVQIGSELP
bprc_D521_0984 NIAEVK--MPNRNGMTTKHGFWS---VS-------GKPDVNGNACMHNCVPFVQIGSTLP
lch_Lcho_3783 TIAQAQARMPNRNGMTLDHGMWPGRGLK-----TAAKPDVKVAACMSNCEAEPKVASFLP
reh_H16_A3571 NIAEIQRRMPNRDGMTTGHGLWPGRG----------RPDTRNTACMKDCAGKVAITSSIP
.**: : :***:*** **:* **.. *** :* : * :*
mms_mma_0447 EPSRNAHGNIQLQNRTFGEVRGVDTTKPASTKPISAISADQKLA-MATPAKPAAPAKVDG
har_HEAR1189 EPSRNAHGNIQEQNRSFGEVRGVNTTVPASTTPISSATRKSVVATAATTAPAEAAAKPKA
dar_Daro_3133 EYARTAHGELADQNRNFGAVRGTRTLGPEAAK---------------------KAADAGT
pnu_Pnuc_0802 DYARNAHGNIAEQNRQYGPFRGSDSTKPPLTKLPGASAEG-----LAHASETHASK-KGP
bprc_D521_0984 DFARNAHENIAEQNRMYGPYRGADTSKPPIKQLPGASGEG-----LAHAADTHTSAAKGP
lch_Lcho_3783 DFARNAHGNLAEQTRMVGAQHGVDTTRPPGAAPTLAAAPV---------VAKATDEGAAA
reh_H16_A3571 DYARDAHGELAQQQRSFGPVRGVAAGN--TVSKSAASAP--------------SEPAAPG
: :* ** :: * * * :* :
mms_mma_0447 LALAKQYACVACHGVSNKIIGPGFNEIAAKYKGDAAAPAALTAKIKNGSTGAWGPIPMPA
har_HEAR1189 LGLAKQYACIACHGVSNKIVGPGFNEIAAKYKGDSAAATTLFDKVKNGSSGAWGPVPMPG
dar_Daro_3133 LELATKSGCMACHGMKSKIVGPGYSEVVARYQGQPDAESRLIAKVKAGGQGVWGSIPMPP
pnu_Pnuc_0802 AELFKSENCTACHAMSTKLVGPSVADIAAKYQGQSGALDTLMAKVKNGGSGVWGPIPMPA
bprc_D521_0984 AALFKNENCSACHAPNAKLVGPSIADIAKKYEGQSGAVDRLMAKVKNGGAGVWGSIPMPP
lch_Lcho_3783 LALAAKHTCTACHAVDAKLVGPAFREIGKKHGSRADAVAYLTGKIKSGGTGVWGAIPMPA
reh_H16_A3571 ARLTSQYQCMACHAMDRKLVGPSFADIAGKYKG-QDAHGALARKVKAGGQGAWGSVPMPA
* . * ***. . *::**. :: :: . * * *:* *. *.**.:***
mms_mma_0447 QAHVKDEDIKTLVGWIIGGAK-
har_HEAR1189 QAHVKDEDVKTLVSWILSGAK-
dar_Daro_3133 NAHVKDEDLKTLVQWILAGSK-
pnu_Pnuc_0802 QSQLSDEDRKALVTWVLSGGK-
bprc_D521_0984 QAQLSDDDRKTLVVWMLSGGK-
lch_Lcho_3783 Q-TLPDADAKLIANWLAAGAKK
reh_H16_A3571 QPQIPDSDVQAMVGWILEAK--
: : * * : :. *: .
例５：系統樹の作成
conf.json
{
"urlStr": "http://ddbj.nig.ac.jp/wabi/clustalw/",
"infile": "/home/hoge/wabi_clustalw_2013-0828-1452-47-561-627715.txt",
"parameters": "-TREE -PIM -OUTPUTTREE=phylip -CLUSTERING=NJ",
"result": "www",
"address": ""
}
例3の整列結果（wabi_clustalw_2013-0828-1452-47-561-627715.txt）から系統樹を作成する場合のサンプル
ここでは、系統樹の作成と同時に percent identity matrix も出力しています。
$ perl clustalw-client3.pl conf.json
Execute multiple sequence alignment.
request-ID: wabi_clustalw_2013-0828-1556-45-267-658015
waiting
finished
ClustalW2 result is outputed to wabi_clustalw_2013-0828-1556-45-267-658015.txt
PIM file is outputed to wabi_clustalw_2013-0828-1556-45-267-658015_pim.txt
$ cat wabi_clustalw_2013-0828-1556-45-267-658015.txt
(
(
mms_mma_0447:0.10748,
har_HEAR1189:0.09643)
:0.08888,
(
(
dar_Daro_3133:0.21190,
(
pnu_Pnuc_0802:0.13187,
bprc_D521_0984:0.12512)
:0.08605)
:0.01023,
reh_H16_A3571:0.23776)
:0.00976,
lch_Lcho_3783:0.23467);
$ cat wabi_clustalw_2013-0828-1556-45-267-658015_pim.txt
#
#
# Percent Identity Matrix - created by Clustal2.1
#
#
1: mms_mma_0447 100 80 57 56 56 58 55
2: har_HEAR1189 80 100 59 58 57 57 57
3: dar_Daro_3133 57 59 100 57 58 53 54
4: pnu_Pnuc_0802 56 58 57 100 74 53 54
5: bprc_D521_0984 56 57 58 74 100 54 55
6: lch_Lcho_3783 58 57 53 53 54 100 52
7: reh_H16_A3571 55 57 54 54 55 52 100
同じ処理をコマンドラインで実行する場合
$ clustalw2 -INFILE=wabi_clustalw_2013-0828-1452-47-561-627715.txt -TREE -PIM -OUTPUTTREE=phylip -CLUSTERING=NJ
例6：ブートストラップ法による系統樹評価
conf.json
{
"urlStr": "http://ddbj.nig.ac.jp/wabi/clustalw/",
"infile": "/home/okuda/data/clustalw_test/wabi_test/wabi_clustalw_2013-0828-1452-47-561-627715.txt",
"parameters": "-BOOTSTRAP=1000 -OUTPUTTREE=phylip -SEED=111 -BOOTLABELS=branch -CLUSTERING=NJ",
"result": "www",
"address": ""
}
例3の整列結果（wabi_clustalw_2013-0828-1452-47-561-627715.txt）から推定した系統樹をブートストラップ法により評価する場合のサンプル
$ perl clustalw-client3.pl conf.json
Execute multiple sequence alignment.
request-ID: wabi_clustalw_2013-0828-1621-44-822-982789
waiting
finished
ClustalW2 result is outputed to wabi_clustalw_2013-0828-1621-44-822-982789.txt
$ cat wabi_clustalw_2013-0828-1621-44-822-982789.txt
(
(
mms_mma_0447:0.10748,
har_HEAR1189:0.09643)
:0.08888[1000],
(
(
dar_Daro_3133:0.21190,
(
pnu_Pnuc_0802:0.13187,
bprc_D521_0984:0.12512)
:0.08605[1000])
:0.01023[621],
reh_H16_A3571:0.23776)
:0.00976[590],
lch_Lcho_3783:0.23467);
同じ処理をコマンドラインで実行する場合
$ clustalw2 -INFILE=wabi_clustalw_2013-0828-1452-47-561-627715.txt -BOOTSTRAP=1000 -OUTPUTTREE=phylip -SEED=111 \
> -BOOTLABELS=branch -CLUSTERING=NJ
例7：配列ファイルのフォーマット変換
conf.json
{
"urlStr": "http://ddbj.nig.ac.jp/wabi/clustalw/",
"infile": "/home/hoge/wabi_clustalw_2013-0828-1452-47-561-627715.txt",
"parameters": "-CONVERT -OUTPUT=FASTA",
"result": "www",
"address": ""
}
例3の整列結果（wabi_clustalw_2013-0828-1452-47-561-627715.txt）をCLUSTAL形式からFASTA形式に変換する場合のサンプル
CLUSTAL, GCG, GDE, PHYLIP, PIR, NEXUS, FASTAの7種類のフォーマットに相互変換が可能である。
$ perl clustalw-client3.pl conf.json
Execute multiple sequence alignment.
request-ID: wabi_clustalw_2013-0828-1706-00-78-535439
waiting
finished
ClustalW2 result is outputed to wabi_clustalw_2013-0828-1706-00-78-535439.txt
$ cat wabi_clustalw_2013-0828-1706-00-78-535439.txt
>mms_mma_0447
--MYRFTKTVVALLLAT-------SGTMALAQAAYTNIGRPATAKEIAAWDIDVRPDFKG
LPPGSGTVAKGMAVWEGKCASCHGTFGESNEVFTPIVGGTTKEDIKSGHVAALSNNKQPQ
RTTIMKVPTVSTLWDYINRAMPWTAPKSLTTEEVYAVTAYILNMAEILPDDFTLSDKNIA
EVQQLMPNRNGMTRNHGMWD---IK-------GKPDVKSVACMKDCKTSTDLRSTLPEPS
RNAHGNIQLQNRTFGEVRGVDTTKPASTKPISAISADQKLA-MATPAKPAAPAKVDGLAL
AKQYACVACHGVSNKIIGPGFNEIAAKYKGDAAAPAALTAKIKNGSTGAWGPIPMPAQAH
VKDEDIKTLVGWIIGGAK-
>har_HEAR1189
--MSRFTKTVVALALVA-------TGAIACAQTAYPHIGRTATEKEIAAWDIDVRPDFKG
LPKGSGTVSKGMEVWEGKCASCHGTFGESNEVFTPIVGGTTKEDVKTGRVAALATNKQPQ
RTTMMKVATVSTLWDYINRAMPWTAPKSLTTEEVYAVTAYILNMSEVLPDDFTLSDKNIA
EVQKLMPNRNGMTQKHGMWD---VK-------GKPDVKSVACMKDCQVSGDIRSSLPEPS
RNAHGNIQEQNRSFGEVRGVNTTVPASTTPISSATRKSVVATAATTAPAEAAAKPKALGL
AKQYACIACHGVSNKIVGPGFNEIAAKYKGDSAAATTLFDKVKNGSSGAWGPVPMPGQAH
VKDEDVKTLVSWILSGAK-
>dar_Daro_3133
--MSRFSKTILVLALLG-------ASSTGFSFENFKGVGRQATPAEVKAWDIDVRPDFKG
LPKGKGNVERGNELFEEKCASCHGSFGESNEVFTPLAGGTTKDDIKTGRVKGLSSGELPQ
RTTFTKVATISTVFDYIQRAMPWTAPKSLKPDDVYAILAYLLNLQEIVPADFELSDRNIA
DVQKLLPNRNGMTTDHGLWPGASAKKGGIGNGGIPDVKNVACMKNCKPEVQIGSTLPEYA
RTAHGELADQNRNFGAVRGTRTLGPEAAK---------------------KAADAGTLEL
ATKSGCMACHGMKSKIVGPGYSEVVARYQGQPDAESRLIAKVKAGGQGVWGSIPMPPNAH
VKDEDLKTLVQWILAGSK-
>pnu_Pnuc_0802
--MFKLAKVAKFTLFAVTTFFAVGSVVAQNSSTHYPGIGRDATPAEVAAWDIDVRPDFKG
LPKGSGSVEKGQQLWEAKCSVCHGTFGESNEIFTPIIGGTTTDDIKTGRVASLSDRKQPQ
RTTIMKVATVSSLWDYIYRAMPWNAPRSLTPDDTFALVAYLLNMAEVVPDDFVLSNTNIA
EVQKRMPNRNGMTLKHGLWN---SK-------GTPDVHATACMTNCVQFVQIGSELPDYA
RNAHGNIAEQNRQYGPFRGSDSTKPPLTKLPGASAEG-----LAHASETHASK-KGPAEL
FKSENCTACHAMSTKLVGPSVADIAAKYQGQSGALDTLMAKVKNGGSGVWGPIPMPAQSQ
LSDEDRKALVTWVLSGGK-
>bprc_D521_0984
--MFKLDKFSISLGFAALIAITAQAALAQSGSAKFPGIGRAATPAEVAAWDIDVRPDFKG
LPKGSGSVEKGQVIWEAKCASCHGTFGESNEIFTPIAGGTTKDDVKTGRVASLKDMKQPQ
RTTLMKVPTVSTLWDYIYRAMPWNAPRSLTPDDTYALVAFILSLGEIVPDDFVLSDKNIA
EVK--MPNRNGMTTKHGFWS---VS-------GKPDVNGNACMHNCVPFVQIGSTLPDFA
RNAHENIAEQNRMYGPYRGADTSKPPIKQLPGASGEG-----LAHAADTHTSAAKGPAAL
FKNENCSACHAPNAKLVGPSIADIAKKYEGQSGAVDRLMAKVKNGGAGVWGSIPMPPQAQ
LSDDDRKTLVVWMLSGGK-
>lch_Lcho_3783
--MSSSPKWLAAAVLAL-------AAAGSLAQVTAVGIGRAATEKEIKAWDIDVRPDFKG
LPKGSGTVEQGMEVWEAKCAHCHGVFGESNEVFSPLVGGTTADDVKTGHVARLNDPTFPG
RTTLMKVATVSTLWDYINRAMPWTAPKSLKTDEVYAVTAYLLNMGDVLPAGFVLSDQTIA
QAQARMPNRNGMTLDHGMWPGRGLKT-----AAKPDVKVAACMSNCEAEPKVASFLPDFA
RNAHGNLAEQTRMVGAQHGVDTTRPPGAAPTLAAAP---------VVAKATDEGAAALAL
AAKHTCTACHAVDAKLVGPAFREIGKKHGSRADAVAYLTGKIKSGGTGVWGAIPMPAQT-
LPDADAKLIANWLAAGAKK
>reh_H16_A3571
MSMWAELRTAAALVLAAVS----AAPAWAGTADARAALGRTATPAEVAAWDIDVRPDFQG
LPRGSGTVAQGQKVWDGKCASCHGDFGESNEVFTPLVGGTTAEDIRRGRVAGMTGN-QPY
RTTLMKVSTVSTLWDYIHRAMPWNAPKSLSVGDVYAVTAYMLHLGEVVPADFTLSDANIA
EIQRRMPNRDGMTTGHGLWP---GR-------GRPDTRNTACMKDCAGKVAITSSIPDYA
RDAHGELAQQQRSFGPVRGVAAGNTVSKS----------------AASAPSEPAAPGARL
TSQYQCMACHAMDRKLVGPSFADIAGKYKGQ-DAHGALARKVKAGGQGAWGSVPMPAQPQ
IPDSDVQAMVGWILEAK--
同じ処理をコマンドラインで実行する場合
$ clustalw2 -INFILE=wabi_clustalw_2013-0828-1452-47-561-627715.txt -CONVERT -OUTPUT=FASTA
例8：custom weight matrixを使用したmultiple alignment
conf.json
{
"urlStr": "http://ddbj.nig.ac.jp/wabi/clustalw/",
"infile": "/home/okuda/data/clustalw_test/wabi_test/cyc_aa.fasta",
"pwaamatrix": "/home/okuda/data/clustalw_test/wabi_test/blosum40.txt",
"aamatrix": "/home/okuda/data/clustalw_test/wabi_test/blosum40.txt",
"parameters": "",
"result": "www",
"address": ""
}
# Matrix made by matblas from blosum40.iij
# * column uses minimum score
# BLOSUM Clustered Scoring Matrix in 1/4 Bit Units
# Blocks Database = /data/blocks_5.0/blocks.dat
# Cluster Percentage: >= 40
# Entropy = 0.2851, Expected = -0.2090
A R N D C Q E G H I L K M F P S T W Y V B Z X *
A 5 -2 -1 -1 -2 0 -1 1 -2 -1 -2 -1 -1 -3 -2 1 0 -3 -2 0 -1 -1 0 -6
R -2 9 0 -1 -3 2 -1 -3 0 -3 -2 3 -1 -2 -3 -1 -2 -2 -1 -2 -1 0 -1 -6
N -1 0 8 2 -2 1 -1 0 1 -2 -3 0 -2 -3 -2 1 0 -4 -2 -3 4 0 -1 -6
D -1 -1 2 9 -2 -1 2 -2 0 -4 -3 0 -3 -4 -2 0 -1 -5 -3 -3 6 1 -1 -6
C -2 -3 -2 -2 16 -4 -2 -3 -4 -4 -2 -3 -3 -2 -5 -1 -1 -6 -4 -2 -2 -3 -2 -6
Q 0 2 1 -1 -4 8 2 -2 0 -3 -2 1 -1 -4 -2 1 -1 -1 -1 -3 0 4 -1 -6
E -1 -1 -1 2 -2 2 7 -3 0 -4 -2 1 -2 -3 0 0 -1 -2 -2 -3 1 5 -1 -6
G 1 -3 0 -2 -3 -2 -3 8 -2 -4 -4 -2 -2 -3 -1 0 -2 -2 -3 -4 -1 -2 -1 -6
H -2 0 1 0 -4 0 0 -2 13 -3 -2 -1 1 -2 -2 -1 -2 -5 2 -4 0 0 -1 -6
I -1 -3 -2 -4 -4 -3 -4 -4 -3 6 2 -3 1 1 -2 -2 -1 -3 0 4 -3 -4 -1 -6
L -2 -2 -3 -3 -2 -2 -2 -4 -2 2 6 -2 3 2 -4 -3 -1 -1 0 2 -3 -2 -1 -6
K -1 3 0 0 -3 1 1 -2 -1 -3 -2 6 -1 -3 -1 0 0 -2 -1 -2 0 1 -1 -6
M -1 -1 -2 -3 -3 -1 -2 -2 1 1 3 -1 7 0 -2 -2 -1 -2 1 1 -3 -2 0 -6
F -3 -2 -3 -4 -2 -4 -3 -3 -2 1 2 -3 0 9 -4 -2 -1 1 4 0 -3 -4 -1 -6
P -2 -3 -2 -2 -5 -2 0 -1 -2 -2 -4 -1 -2 -4 11 -1 0 -4 -3 -3 -2 -1 -2 -6
S 1 -1 1 0 -1 1 0 0 -1 -2 -3 0 -2 -2 -1 5 2 -5 -2 -1 0 0 0 -6
T 0 -2 0 -1 -1 -1 -1 -2 -2 -1 -1 0 -1 -1 0 2 6 -4 -1 1 0 -1 0 -6
W -3 -2 -4 -5 -6 -1 -2 -2 -5 -3 -1 -2 -2 1 -4 -5 -4 19 3 -3 -4 -2 -2 -6
Y -2 -1 -2 -3 -4 -1 -2 -3 2 0 0 -1 1 4 -3 -2 -1 3 9 -1 -3 -2 -1 -6
V 0 -2 -3 -3 -2 -3 -3 -4 -4 4 2 -2 1 0 -3 -1 1 -3 -1 5 -3 -3 -1 -6
B -1 -1 4 6 -2 0 1 -1 0 -3 -3 0 -3 -3 -2 0 0 -4 -3 -3 5 2 -1 -6
Z -1 0 0 1 -3 4 5 -2 0 -4 -2 1 -2 -4 -1 0 -1 -2 -2 -3 2 5 -1 -6
X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 0 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -6
* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1
pairwise alignment と multiple alignment で built-in ではない weight matrix を使用する場合のサンプル
実際には clustalw2 には BLOSUM series の weight matrix は入っていますが、ここではユーザー定義ファイルとして用意して使用しています。
$ perl clustalw-client3.pl conf.json
Execute multiple sequence alignment.
request-ID: wabi_clustalw_2013-0828-1815-17-562-701719
waiting
finished
ClustalW2 result is outputed to wabi_clustalw_2013-0828-1815-17-562-701719.txt
Guide Tree 1 is outputed to wabi_clustalw_2013-0828-1815-17-562-701719_guidetree1.txt
$ cat wabi_clustalw_2013-0828-1815-17-562-701719.txt
CLUSTAL 2.1 multiple sequence alignment
mms_mma_0447 -------MYRFTKTVVALLLATSGTMALAQAAYTNIGRPATAKEIAAWDIDVRPDFKGLP
har_HEAR1189 -------MSRFTKTVVALALVATGAIACAQTAYPHIGRTATEKEIAAWDIDVRPDFKGLP
dar_Daro_3133 -------MSRFSKTILVLALLGASSTGFSFENFKGVGRQATPAEVKAWDIDVRPDFKGLP
pnu_Pnuc_0802 MFKLAKVAKFTLFAVTTFFAVGSVVAQNSSTHYPGIGRDATPAEVAAWDIDVRPDFKGLP
bprc_D521_0984 MFKLDKFSISLGFAALIAITAQAALAQSGSAKFPGIGRAATPAEVAAWDIDVRPDFKGLP
: : . : :** ** *: **************
mms_mma_0447 PGSGTVAKGMAVWEGKCASCHGTFGESNEVFTPIVGGTTKEDIKSGHVAALSNNKQPQRT
har_HEAR1189 KGSGTVSKGMEVWEGKCASCHGTFGESNEVFTPIVGGTTKEDVKTGRVAALATNKQPQRT
dar_Daro_3133 KGKGNVERGNELFEEKCASCHGSFGESNEVFTPLAGGTTKDDIKTGRVKGLSSGELPQRT
pnu_Pnuc_0802 KGSGSVEKGQQLWEAKCSVCHGTFGESNEIFTPIIGGTTTDDIKTGRVASLSDRKQPQRT
bprc_D521_0984 KGSGSVEKGQVIWEAKCASCHGTFGESNEIFTPIAGGTTKDDVKTGRVASLKDMKQPQRT
*.*.* :* ::* **: ***:******:***: ****.:*:*:*:* .* : ****
mms_mma_0447 TIMKVPTVSTLWDYINRAMPWTAPKSLTTEEVYAVTAYILNMAEILPDDFTLSDKNIAEV
har_HEAR1189 TMMKVATVSTLWDYINRAMPWTAPKSLTTEEVYAVTAYILNMSEVLPDDFTLSDKNIAEV
dar_Daro_3133 TFTKVATISTVFDYIQRAMPWTAPKSLKPDDVYAILAYLLNLQEIVPADFELSDRNIADV
pnu_Pnuc_0802 TIMKVATVSSLWDYIYRAMPWNAPRSLTPDDTFALVAYLLNMAEVVPDDFVLSNTNIAEV
bprc_D521_0984 TLMKVPTVSTLWDYIYRAMPWNAPRSLTPDDTYALVAFILSLGEIVPDDFVLSDKNIAEV
*: **.*:*:::*** *****.**:**..::.:*: *::*.: *::* ** **: ***:*
mms_mma_0447 QQLMPNRNGMTRNHGMWDIK----------GKPDVKSVACMKDCKTSTDLRSTLPEPSRN
har_HEAR1189 QKLMPNRNGMTQKHGMWDVK----------GKPDVKSVACMKDCQVSGDIRSSLPEPSRN
dar_Daro_3133 QKLLPNRNGMTTDHGLWPGASAKKGGIGNGGIPDVKNVACMKNCKPEVQIGSTLPEYART
pnu_Pnuc_0802 QKRMPNRNGMTLKHGLWNSK----------GTPDVHATACMTNCVQFVQIGSELPDYARN
bprc_D521_0984 K--MPNRNGMTTKHGFWSVS----------GKPDVNGNACMHNCVPFVQIGSTLPDFARN
: :******* .**:* * ***: *** :* :: * **: :*.
mms_mma_0447 AHGNIQLQNRTFGEVRGVDTTKPASTKPISAISADQKLAMATPAKPAAP-AKVDGLALAK
har_HEAR1189 AHGNIQEQNRSFGEVRGVNTTVPASTTPISSATRKSVVATAATTAPAEAAAKPKALGLAK
dar_Daro_3133 AHGELADQNRNFGAVRGTRTLGPEAAKKAADAG---------------------TLELAT
pnu_Pnuc_0802 AHGNIAEQNRQYGPFRGSDSTKPPLTKLPGASAEGLAHASETHASK------KGPAELFK
bprc_D521_0984 AHENIAEQNRMYGPYRGADTSKPPIKQLPGASGEGLAHAADTHTSAA-----KGPAALFK
** :: *** :* ** : * . * .
mms_mma_0447 QYACVACHGVSNKIIGPGFNEIAAKYKGDAAAPAALTAKIKNGSTGAWGPIPMPAQAHVK
har_HEAR1189 QYACIACHGVSNKIVGPGFNEIAAKYKGDSAAATTLFDKVKNGSSGAWGPVPMPGQAHVK
dar_Daro_3133 KSGCMACHGMKSKIVGPGYSEVVARYQGQPDAESRLIAKVKAGGQGVWGSIPMPPNAHVK
pnu_Pnuc_0802 SENCTACHAMSTKLVGPSVADIAAKYQGQSGALDTLMAKVKNGGSGVWGPIPMPAQSQLS
bprc_D521_0984 NENCSACHAPNAKLVGPSIADIAKKYEGQSGAVDRLMAKVKNGGAGVWGSIPMPPQAQLS
. * ***. . *::**. ::. :*:*:. * * *:* *. *.**.:*** ::::.
mms_mma_0447 DEDIKTLVGWIIGGAK
har_HEAR1189 DEDVKTLVSWILSGAK
dar_Daro_3133 DEDLKTLVQWILAGSK
pnu_Pnuc_0802 DEDRKALVTWVLSGGK
bprc_D521_0984 DDDRKTLVVWMLSGGK
*:* *:** *::.*.*
同じ処理をコマンドラインで実行する場合
$ clustalw2 -INFILE=cyc_aa.fasta -PWMATRIX=blosum40.txt -MATRIX=blosum40.txt