getentry HELP

About getentry

• "getentry" is a DDBJ flat file search system, by accession numbers.
• "getentry" is available from WebAPI program, as well as a simple web form, which call up the data directly.
• WebAPI also provides a new function "gethistory" (revision history search)
• "Keyword search of DDBJ flat file" which was implemented in the former getentry (-2012.02) can is avialable in the ARSA

Search by web input form

URL: http://getentry.ddbj.nig.ac.jp/top-e.html

WebAPI programs and URLs

WebAPI of new getentry consists of two following programs.

* Update history of the amino acid sequence derived from the Patent Office has not been taken so far.

How to specify the parameter

There are the following 2 methods.

Specifiable parameters

getentry

• accession number(mandatory): Specify the accession number for searching.
• database(optional): Specify the database for searching.
• revision(optional): Search for the specified revision.
• format(optional): Specify the output format for the result.
• filetype(optional): Specify the filetype for the output.
• show_suppressed(optional): To display the data for the replaced or suppressed.
• limit(optional): Sets an upper limit of the data acquisition.

accession number(mandatory): Specify the accession number for searching.

database(optional): Specify the database for searching.

revision(optional): Search for the specified revision.

format(optional): Specify the output format for the result.

LOCUS       AB628096                 390 bp    RNA     linear   VRL 24-FEB-2012
DEFINITION  Human rhinovirus C gene for polyprotein, partial cds, strain:
            HRV/Yamaguchi/2010/89.
ACCESSION   AB628096
VERSION     AB628096.1
KEYWORDS    .
SOURCE      Human rhinovirus C
  ORGANISM  Human rhinovirus C
            Viruses; ssRNA positive-strand viruses, no DNA stage;
            Picornavirales; Picornaviridae; Enterovirus.
REFERENCE   1  (bases 1 to 390)
  AUTHORS   Kobayashi,M., Arakawa,M., Okamoto,R., Tsukagoshi,H., Ryo,A.,
            Mizuta,K., Hasegawa,S., Hirano,R., Wakiguchi,H., Kudo,K.,
            Tanaka,R., Morita,Y., Noda,M., Kozawa,K., Ichiyama,T., Shirabe,K.
            and Kimura,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-MAY-2011) to the DDBJ/EMBL/GenBank databases.
            Contact:Miho Kobayashi
            Gunma Prefectural Institute of Public Health and Environmental
            Sciences; Kamiokimachi 378, Maebashi, Gunma 371-0052, Japan
REFERENCE   2  
  AUTHORS   Arakawa,M., Okamoto-Nakagawa,R., Toda,S., Tsukagoshi,H.,
            Kobayashi,M., Ryo,A., Mizuta,K., Hasegawa,S., Hirano,R.,
            Wakiguchi,H., Kudo,K., Tanaka,R., Morita,Y., Noda,M., Kozawa,K.,
            Ichiyama,T., Shirabe,K. and Kimura,H.
  TITLE     Molecular epidemiological study of human rhinovirus species A, B
            and C from patients with acute respiratory illnesses in Japan
  JOURNAL   J. Med. Microbiol. 61, 410-419 (2012)
  REMARK    DOI:10.1099/jmm.0.035006-0
COMMENT     
FEATURES             Location/Qualifiers
     source          1..390
                     /collection_date="14-Jan-2010"
                     /country="Japan:Yamaguchi"
                     /db_xref="taxon:463676"
                     /host="Homo sapiens"
                     /isolation_source="Nasopharyngeal swab"
                     /mol_type="genomic RNA"
                     /organism="Human rhinovirus C"
                     /strain="HRV/Yamaguchi/2010/89"
     CDS             1..>390
                     /codon_start=1
                     /product="polyprotein"
                     /protein_id="BAK22546.1"
                     /transl_table=1
                     /translation="MGAQVSKQNVGSHENSVSATGGSVIKYFNINYYKDSASSGLTKQ
                     DFSQDPSKFTQPLAEALTNPALMSPTVEACGMSDRLKQITIGNSTITTQDTLNSILAY
                     GEWPKYLSDLDASSVDKPTHPETSSDRF"
BASE COUNT          124 a           95 c           77 g           94 t
ORIGIN      
        1 atgggcgcac aggtgagcaa gcaaaatgtc ggctcgcacg aaaattcagt ctcagccacg
       61 ggtggatccg tgattaagta tttcaacatc aattactaca aggattctgc tagctctggc
      121 ttgactaaac aagatttttc ccaagaccca tcgaaattca cacaacctct agcagaagca
      181 cttacaaatc cagctttaat gtcaccaact gttgaagcat gtgggatgtc cgataggctt
      241 aaacaaatta ctatcgggaa ttccactata acaacacaag atacactaaa ctctatactg
      301 gcatatgggg agtggcccaa atacttgagt gacctggacg cttcctcagt ggataagcct
      361 acccacccag agacatcatc tgatagattt
//
 

                           

<?xml version="1.0"?>

<!DOCTYPE INSDSet SYSTEM "INSD_INSDSeq.dtd">
-<INSDSet>
 -<INSDSeq> <INSDSeq_locus>AB601234</INSDSeq_locus>
  <INSDSeq_length>358</INSDSeq_length>
   <INSDSeq_moltype>DNA</INSDSeq_moltype>
    <INSDSeq_topology>linear</INSDSeq_topology>
     <INSDSeq_division>PLN</INSDSeq_division>
      <INSDSeq_update-date>18-MAY-2011</INSDSeq_update-date>
       <INSDSeq_definition>Ainsliaea faurieana chs gene for chalcone ......
         <INSDSeq_primary-accession>AB601234</INSDSeq_primary-accession>
         <INSDSeq_accession-version>AB601234.1</INSDSeq_accession-version>
          <INSDSeq_source>Ainsliaea faurieana</INSDSeq_source>
           <INSDSeq_organism>Ainsliaea faurieana</INSDSeq_organism>
            <INSDSeq_taxonomy>Eukaryota; Viridiplantae; Streptophyta; .......
             -<INSDSeq_references>
              -<INSDReference>
              <INSDReference_reference>1</INSDReference_reference>
               <INSDReference_position>1..358</INSDReference_position>
                -<INSDReference_authors> <INSDAuthor>Mitsui,Y.</INSDAuthor>
                 <INSDAuthor>Setoguchi,H.</INSDAuthor> </INSDReference_authors>
                  <INSDReference_title>Direct Submission</INSDReference_title>
                   <INSDReference_journal>Submitted (17-NOV-2010) to the DDBJ/.....
                    -<INSDReference>

                                   -------   以下略    -----

 >HE963104-1|CCJ27876.1|111|<1..111|Streptococcus thermophilus|predicted.....
gggttgtcctgtgatgagggaatgctggcagtaggaggacttggtgctgtaggtggcccg
tggggagctgtcggtggggtgttagtaggtgcagccttatactgtttctaa

>HE963104-2|CCJ27877.1|201|130..330|Streptococcus thermophilus|hypothetical.....
atgaataataaacaacttgaaagatttaaaaaactggatacaaatgcattgtctaatgta
agtggtcaaggctatggtgctcaatgtgttattggtactgccggaatgacgattgtcggt
gcagctttctttggcatcgcaggtgcaggagctggatttgcaggcggtagcacagcattt
tgttatggtacagctgaataa

>HE963104-3|CCJ27878.1|219|686..>904|Streptococcus thermophilus|.....
atggcaactcaaacaattgaaaactttaacacccttaacctcgaaacacttgctagtgtt
gaaggaggtggatgtggttggagaggcgcaggtggagcgactgttcaaggagctatcggg
ggagcgtttggaggtaatgtagttttaccagttgtaggctcagttcctggttatctagct
ggtggtgttctaggtggtgcaggtggtactgttgcctat
 

filetype(optional): Specify the filetype for the result.

Following is shown on the display

LOCUS       FW383979                2675 bp    DNA     linear   PAT 14-OCT-2010
DEFINITION  JP 2006521812-A/1: GENETIC POLYMORPHISMS ASSOCIATED WITH RHEUMATOID
            ARTHRITIS, METHODS OF DETECTION AND USES THEREOF.
ACCESSION   FW383979
VERSION     FW383979.1
KEYWORDS    JP 2006521812-A/1.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 2675)
  AUTHORS   Alexander,H.C., Bigobikku,A.B. and Kagiru,M.
  TITLE     GENETIC POLYMORPHISMS ASSOCIATED WITH RHEUMATOID
            ARTHRITIS, METHODS 
            OF DETECTION AND USES THEREOF 
  JOURNAL   Patent: JP 2006521812-A 1 28-Sep-2006;
            APLERA CORPORATION
COMMENT     OS   Homo sapiens
            PN   JP 2006521812-A/1
            PD   28-Sep-2006
                               
 

show_suppressed (optional): To display the suppressed data.

limit(optional): Sets an upper limit of the data acquisition.

It may take a long time to display a large number of results.
According to the performance of the browser, all of that might not be displayed.

gethistory

• accession number(mandatory): Specify the accession number for searching.
• database(optional): Specify the database for searching.
• filetype(optional): Specify the filetype for the result.

accession number(mandatory): Specify the accession number for searching.

Specification method is the same as getentry.

History of the amino acid sequence derived from the Patent Office is not available.
 
 

database(optional): Specify the database for searching.

If the specified database does not correspond to the history management, and returns an empty result.

 

 
filetype(optional): Specify the filetype for the result.

How to Create Links to DDBJ Entries

You can create links to individual DDBJ entries.

• http://getentry.ddbj.nig.ac.jp/getentry?database=database name&accession_number=accession number&additional parameters (optional)
• http://getentry.ddbj.nig.ac.jp/getentry/database name/accession number
• http://getentry.ddbj.nig.ac.jp/getentry/database name/accession number/?additional parameters (optional)

For example,

As a practical case, please crick the following number to see how the entry can be viewed.

Creating links to DRA entries is different from the above method. Please refer to the DRA Web site.

If you build your own website, Please use this method.