$export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH #今の私の設定環境だと、結局これをシェルを開いたら最初にいれないといけないみたい。。。
$wossname #EMBOSSは多数の解析のためのコマンド群からなっている。これを調べるにはwossnameコマンドを使う。
Finds programs by keywords in their short description #ここで何も入れないと、全部のコマンドが表示されていくる。
Text to search for, or blank to list all programs:
ACD
acdc Test an application ACD file
acdpretty Correctly reformat an application ACD file
acdtable Generate an HTML table of parameters from an application ACD file
acdtrace Trace processing of an application ACD file (for testing)
acdvalid Validate an application ACD file
$infoseq refseq:NM_138712 #infoseqコマンドを実行することでNM_138712に関するざっくりとした説明文が見れる。
Display basic information about sequences
USA Database Name Accession Type Length %GC Organism Description
refseq-id:NM_138712 refseq NM_138712 NM_138712 N 1892 48.10 Homo sapiens (human) Homo sapiens peroxisome proliferator-activated receptor gamma (PPARG), transcript variant 1, mRNA.
#インターネット経由で配列を読み込んでみる。
$seqret refseq:NM_138712 -outseq hsa_pparg.nt
Reads and writes (returns) sequences
$less hsa_pparg.nt
>NM_138712 NM_138712.3 Homo sapiens peroxisome proliferator-activated receptor gamma (PPARG), transcript variant 1, mRNA.
ggcgcccgcgcccgcccccgcgccgggcccggctcggcccgacccggctccgccgcgggc
aggcggggcccagcgcactcggagcccgagcccgagccgcagccgccgcctggggcgctt
gggtcggcctcgaggacaccggagaggggcgccacgccgccgtggccgcagatttgaaag
aagccaacactaaaccacaaatatacaacaaggccattttctcaaacgagagtcagcctt
taacgaaatgaccatggttgacacagagatgccattctggcccaccaactttgggatcag
ctccgtggatctctccgtaatggaagaccactcccactcctttgatatcaagcccttcac
tactgttgacttctccagcatttctactccacattacgaagacattccattcacaagaac
agatccagtggttgcagattacaagtatgacctgaaacttcaagagtaccaaagtgcaat
caaagtggagcctgcatctccaccttattattctgagaagactcagctctacaataagcc
tcatgaagagccttccaactccctcatggcaattgaatgtcgtgtctgtggagataaagc
ttctggatttcactatggagttcatgcttgtgaaggatgcaagggtttcttccggagaac
aatcagattgaagcttatctatgacagatgtgatcttaactgtcggatccacaaaaaaag
tagaaataaatgtcagtactgtcggtttcagaaatgccttgcagtggggatgtctcataa
tgccatcaggtttgggcggatgccacaggccgagaaggagaagctgttggcggagatctc
cagtgatatcgaccagctgaatccagagtccgctgacctccgggccctggcaaaacattt
gtatgactcatacataaagtccttcccgctgaccaaagcaaaggcgagggcgatcttgac
aggaaagacaacagacaaatcaccattcgttatctatgacatgaattccttaatgatggg
agaagataaaatcaagttcaaacacatcacccccctgcaggagcagagcaaagaggtggc
catccgcatctttcagggctgccagtttcgctccgtggaggctgtgcaggagatcacaga
gtatgccaaaagcattcctggttttgtaaatcttgacttgaacgaccaagtaactctcct
caaatatggagtccacgagatcatttacacaatgctggcctccttgatgaataaagatgg
ggttctcatatccgagggccaaggcttcatgacaagggagtttctaaagagcctgcgaaa
gccttttggtgactttatggagcccaagtttgagtttgctgtgaagttcaatgcactgga
attagatgacagcgacttggcaatatttattgctgtcattattctcagtggagaccgccc
aggtttgctgaatgtgaagcccattgaagacattcaagacaacctgctacaagccctgga
gctccagctgaagctgaaccaccctgagtcctcacagctgtttgccaagctgctccagaa
aatgacagacctcagacagattgtcacggaacacgtgcagctactgcaggtgatcaagaa
gacggagacagacatgagtcttcacccgctcctgcaggagatctacaaggacttgtacta
gcagagagtcctgagccactgccaacatttcccttcttccagttgcactattctgaggga
aaatctgacacctaagaaatttactgtgaaaaagcattttaaaaagaaaaggttttagaa
tatgatctattttatgcatattgtttataaagacacatttacaatttacttttaatatta
aaaattaccatattatgaaattgctgatagta
hsa_pparg.nt (END)
#"q"を一発入力してやれば、$の画面に戻ります♪
#こんなことともできるようです。
$ seqret swissprot:BACE*HUMAN -out=BACE_HUMAN.dat
Reads and writes (returns) sequences
@tetsuo-desktop:~$ more BACE_HUMAN.dat
>BACE1_HUMAN P56817 Beta-secretase 1 (3.4.23.46) (Aspartyl protease 2) (ASP2) (A
sp 2) (Beta-site amyloid precursor protein cleaving enzyme 1) (Beta-site APP cle
aving enzyme 1) (Memapsin-2) (Membrane-associated aspartic protease 2) (Precurso
r)
MAQALPWLLLWMGAGVLPAHGTQHGIRLPLRSGLGGAPLGLRLPRETDEEPEEPGRRGSF
VEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSST
YRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGIL
GLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGI
DHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKK
VFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRIT
ILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSAC
HVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDESTLMTIAYVMAAICALFMLPLCLMVCQW
CCLRCLRQQHDDFADDISLLK
>BACE2_HUMAN Q9Y5Z0 Beta-secretase 2 (3.4.23.45) (Aspartic-like protease 56 kDa)
(Aspartyl protease 1) (ASP1) (Asp 1) (Beta-site amyloid precursor protein cleav
ing enzyme 2) (Beta-site APP cleaving enzyme 2) (Down region aspartic protease)
(DRAP) (Memapsin-1) (Membrane-associated aspartic protease 1) (Theta-secretase)
(Precursor)
MGALARALLLPLLAQWLLRAAPELAPAPFTLPLRVAAATNRVVAPTPGPGTPAERHADGL
ALALEPALASPAGAANFLAMVDNLQGDSGRGYYLEMLIGTPPQKLQILVDTGSSNFAVAG
TPHSYIDTYFDTERSSTYRSKGFDVTVKYTQGSWTGFVGEDLVTIPKGFNTSFLVNIATI
FESENFFLPGIKWNGILGLAYATLAKPSSSLETFFDSLVTQANIPNVFSMQMCGAGLPVA
GSGTNGGSLVLGGIEPSLYKGDIWYTPIKEEWYYQIEILKLEIGGQSLNLDCREYNADKA
IVDSGTTLLRLPQKVFDAVVEAVARASLIPEFSDGFWTGSQLACWTNSETPWSYFPKISI
YLRDENSSRSFRITILPQLYIQPMMGAGLNYECYRFGISPSTNALVIGATVMEGFYVIFD
RAQKRVGFAASPCAEIAGAAVSEISGPFSTEDVASNCVPAQSLSEPILWIVSYALMSVCG
AILLVLIVLLLLPFRCQRRPRDPEVVNDESSLVRHRWK
EMBOSS恐ろしや。GUIでこの作業をするとちょっと面倒くさいなあと思います。
