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2009年5月20日

EMBOSSを試す その2    

さて、インストールしたEMBOSS、試しに何か使ってみようといいネタ探していたらseqretというコマンドがよさそうなのでこれを試す。seqretは、配列をFASTA形式で取得するコマンドのよう。

$ seqret --help
  Standard (Mandatory) qualifiers:
  [-sequence] seqall (Gapped) sequence(s) filename and optional
  format, or reference (input USA)
  [-outseq] seqoutall [.] Sequence set(s)
  filename and optional format (output USA)

  Additional (Optional) qualifiers: (none)
  Advanced (Unprompted) qualifiers:
  -feature boolean Use feature information
  -firstonly boolean [N] Read one sequence and stop

  General qualifiers:
  -help boolean Report command line options. More
  information on associated and general
  qualifiers can be found with -help -verbose

ちょうど、巷で話題になっている豚インフルの配列が公開されているので、それを取ってみることに。

$ seqret genbank:GQ149630
Reads and writes (returns) sequences
output sequence(s) [gq149630.fasta]:

このプログラム、ファイルとして出力されるようにプログラムされていて標準出力には出てこない。

$ cat gq149630.fasta
>GQ149630 GQ149630.1 Influenza A virus (A/Mexico/4603/2009(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds.
atgaaggcaatactagtagttctgctatatacatttgcaaccgcaaatgcagacacatta
tgtataggttatcatgcgaacaattcaacagacactgtagacacagtactagaaaagaat
gtaacagtaacacactctgttaaccttctagaagacaagcataacgggaaactatgcaaa
ctaagaggggtagccccattgcatttgggtaaatgtaacattgctggctggatcctggga
aatccagagtgtgaatcactctccacagcaagctcatggtcctacattgtggaaacatct
agttcagacaatggaacgtgttacccaggagatttcatcgattatgaggagctaagagag
caattgagctcagtgtcatcatttgaaaggtttgagatattccccaagacaagttcatgg
cccaatcatgactcgaacaaaggtgtaacggcagcatgtcctcatgctggagcaaaaagc
ttctacaaaaatttaatatggctagttaaaaaaggaaattcatacccaaagctcagcaaa
tcctacattaatgataaagggaaagaagtcctcgtgctatggggcattcaccatccatct
actagtgctgaccaacaaagtctctatcagaatgcagatgcatatgtttttgtggggtca
tcaagatacagcaagaagttcaagccggaaatagcaataagacccaaagtgagggatcaa
gaagggagaatgaactattactggacactagtagagccgggagacaaaataacattcgaa
gcaactggaaatctagtggtaccgagatatgcattcgcaatggaaagaaatgctggatct
ggtattatcatttcagatacaccagtccacgattgcaatacaacttgtcagacacccaag
ggtgctataaacaccagcctcccatttcagaatatacatccgatcacaattggaaaatgt
ccaaaatatgtaaaaagcacaaaattgagactggccacaggattgaggaatgtcccgtct
attcaatctagaggcctatttggggccattgccggtttcattgaaggggggtggacaggg
atggtagatggatggtacggttatcaccatcaaaatgagcaggggtcaggatatgcagcc
gacctgaagagcacacagaatgccattgacgagattactaacaaagtaaattctgttatt
gaaaagatgaatacacagttcacagcagtaggtaaagagttcaaccacctggaaaaaaga
atagagaatttaaataaaaaagttgatgatggtttcctggacatttggacttacaatgcc
gaactgttggttctattggaaaatgaaagaactttggactaccacgattcaaatgtgaag
aacttatatgaaaaggtaagaagccagttaaaaaacaatgccaaggaaattggaaacggc
tgctttgaattttaccacaaatgcgataacacgtgcatggaaagtgtcaaaaatgggact
tatgactacccaaaatactcagaggaagcaaaattaaacagagaagaaatagatggggta
aagctggaatcaacaaggatttaccagattttggcgatctattcaactgtcgccagttca
ttggtactggtagtctccctgggggcaatcagtttctggatgtgctctaatgggtctcta
cagtgtagaatatgtatttaa

かと思ったら標準出力にも出せた($seqret genbank:GQ149630 stdout)。entretを使うと、全部のデータを出せるらしい。

$ entret genbank:GQ149630 stdout
Retrieves sequence entries from flatfile databases and files
LOCUS GQ149630 1701 bp cRNA linear VRL 13-MAY-2009
DEFINITION Influenza A virus (A/Mexico/4603/2009(H1N1)) segment 4
  hemagglutinin (HA) gene, complete cds.
ACCESSION GQ149630
VERSION GQ149630.1 GI:237511793
DBLINK Project:37813
KEYWORDS .
SOURCE Influenza A virus (A/Mexico/4603/2009(H1N1))
  ORGANISM Influenza A virus (A/Mexico/4603/2009(H1N1))
  Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
  Influenzavirus A.
REFERENCE 1 (bases 1 to 1701)
  AUTHORS Alpuche-Aranda,C.M., Lopez-Gatell,H., Olivera,H., Lopez,I., Shu,B.,
  Balish,A., Garten,R., Smith,C., Emery,S., Barnes,J., Deyde,V.,
  Klimov,A. and Cox,N.
  TITLE Human infection with novel swine H1N1 influenza
  JOURNAL Unpublished
REFERENCE 2 (bases 1 to 1701)
  AUTHORS Alpuche-Aranda,C.M., Lopez-Gatell,H., Olivera,H., Lopez,I., Shu,B.,
  Balish,A., Garten,R., Smith,C., Emery,S., Barnes,J., Deyde,V.,
  Klimov,A. and Cox,N.
  TITLE Direct Submission
  JOURNAL Submitted (13-MAY-2009) WHO Collaborating Center for Surveillance,
  Epidemiology and Control of Influenza, Influenza Division, Centers
  for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta,
  GA 30333, USA
COMMENT Swine influenza A (H1N1) virus isolated during human swine flu
  outbreak of 2009.

  Some of the information does not have GenBank feature identifiers
  and is being provided in the comment section.

  ##EpifluData-START##
  Isolate A/Mexico/4603/2009
  Subtype H1N1
  Segment_name HA
  Host_gender F
  Host_age 59
  Passage_history C1
  Adamantane_resistance resistant
  Zanamivir_resistance sensitive
  Oseltamivir_resistance sensitive
  Country Mexico
  Collection_day 19
  Collection_month 4
  Collection_year 2009
  EPI_accession EPI176604
  ##EpifluData-END##
FEATURES Location/Qualifiers
  source 1..1701
  /organism="Influenza A virus (A/Mexico/4603/2009(H1N1))"
  /mol_type="viral cRNA"
  /strain="A/Mexico/4603/2009"
  /serotype="H1N1"
  /host="Homo sapiens; gender F; age 59"
  /db_xref="taxon:644887"
  /segment="4"
  /country="Mexico"
  /collection_date="19-Apr-2009"
  gene 1..1701
  /gene="HA"
  CDS 1..1701
  /gene="HA"
  /codon_start=1
  /product="hemagglutinin"
  /protein_id="ACQ99608.1"
  /db_xref="GI:237511794"
  /translation="MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVT
  HSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSS
  DNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKS
  FYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADAYVFV
  GSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMER
  NAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATG
  LRNVPSIQSRGLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEI
  TNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENER
  TLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSE
  EAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISFWMCSNGSLQCRICI"
ORIGIN
  1 atgaaggcaa tactagtagt tctgctatat acatttgcaa ccgcaaatgc agacacatta
  61 tgtataggtt atcatgcgaa caattcaaca gacactgtag acacagtact agaaaagaat
  121 gtaacagtaa cacactctgt taaccttcta gaagacaagc ataacgggaa actatgcaaa
  181 ctaagagggg tagccccatt gcatttgggt aaatgtaaca ttgctggctg gatcctggga
  241 aatccagagt gtgaatcact ctccacagca agctcatggt cctacattgt ggaaacatct
  301 agttcagaca atggaacgtg ttacccagga gatttcatcg attatgagga gctaagagag
  361 caattgagct cagtgtcatc atttgaaagg tttgagatat tccccaagac aagttcatgg
  421 cccaatcatg actcgaacaa aggtgtaacg gcagcatgtc ctcatgctgg agcaaaaagc
  481 ttctacaaaa atttaatatg gctagttaaa aaaggaaatt catacccaaa gctcagcaaa
  541 tcctacatta atgataaagg gaaagaagtc ctcgtgctat ggggcattca ccatccatct
  601 actagtgctg accaacaaag tctctatcag aatgcagatg catatgtttt tgtggggtca
  661 tcaagataca gcaagaagtt caagccggaa atagcaataa gacccaaagt gagggatcaa
  721 gaagggagaa tgaactatta ctggacacta gtagagccgg gagacaaaat aacattcgaa
  781 gcaactggaa atctagtggt accgagatat gcattcgcaa tggaaagaaa tgctggatct
  841 ggtattatca tttcagatac accagtccac gattgcaata caacttgtca gacacccaag
  901 ggtgctataa acaccagcct cccatttcag aatatacatc cgatcacaat tggaaaatgt
  961 ccaaaatatg taaaaagcac aaaattgaga ctggccacag gattgaggaa tgtcccgtct
  1021 attcaatcta gaggcctatt tggggccatt gccggtttca ttgaaggggg gtggacaggg
  1081 atggtagatg gatggtacgg ttatcaccat caaaatgagc aggggtcagg atatgcagcc
  1141 gacctgaaga gcacacagaa tgccattgac gagattacta acaaagtaaa ttctgttatt
  1201 gaaaagatga atacacagtt cacagcagta ggtaaagagt tcaaccacct ggaaaaaaga
  1261 atagagaatt taaataaaaa agttgatgat ggtttcctgg acatttggac ttacaatgcc
  1321 gaactgttgg ttctattgga aaatgaaaga actttggact accacgattc aaatgtgaag
  1381 aacttatatg aaaaggtaag aagccagtta aaaaacaatg ccaaggaaat tggaaacggc
  1441 tgctttgaat tttaccacaa atgcgataac acgtgcatgg aaagtgtcaa aaatgggact
  1501 tatgactacc caaaatactc agaggaagca aaattaaaca gagaagaaat agatggggta
  1561 aagctggaat caacaaggat ttaccagatt ttggcgatct attcaactgt cgccagttca
  1621 ttggtactgg tagtctccct gggggcaatc agtttctgga tgtgctctaa tgggtctcta
  1681 cagtgtagaa tatgtattta a
//

By ただ at 23:00 カテゴリー ; 生命科学

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