Last updated:2017.10.3.

ARSA HELP

Searchable DataBases

ARSA retrieves the following databases.
Database Note
DDBJ Release  
DDBJ New (daily updates)  
Amino Acid Patent Sequence data submitted from JPO  
Amino Acid Patent Sequence data submitted from KIPO Update is not periodical

Entries whose accession number is assigned in a different rules from general data, such as WGS(including WGS Scaffold CON), some TSA entries, MGA are not searchable in ARSA.

Quick Search

These are search options and examples. If you click "Search Condition" at the Result page, you can check your entered keyword.
When you use the boolean operators (AND, OR, NOT) in the text box, please write in capitals.

"AND" search(Searchs that contain all search keywords)
Enter all keywords into the text box, separating each word with a space.
Example: Enter lung cancer to the text box, and select "AND" as a boolean operator.
http://ddbj.nig.ac.jp/arsa/search?lang=en&cond=quick_search&query=lung+cancer&operator=AND
The result contains for example,

  • "~ Human lung cancer associated ~" in the DEFINITION.
  • "~ Lung Focal Fibrosis ~" in the FEATURES, and "~ National Cancer Institute ~" in the REFERENCE TITLE.

Partial match search(Searchs that contains the search keyword in a part of a word)

Specify the search keyword containing the wild card *.
Example: Enter HomHom*
http://ddbj.nig.ac.jp/arsa/search?lang=en&cond=quick_search&query=Hom*&operator=AND
The result contains for example,

  • "~ Hominidae; ~" in the SOURCE ORGANISM.
  • "~ higher homolog of ~" in the REFERENCE TITLE.

Phrase search(Searchs keyword in a word order)

Enclose the phrase into double quotation( " ). A character with a special meaning is also searched as a free search keyword.
Example: Enter ""lung cancer""
http://ddbj.nig.ac.jp/arsa/search?lang=en&cond=quick_search&query=%22lung+cancer%22&operator=AND
The result contains for example,

  • 例: DEFINITION に「~ Human lung cancer associated ~」と記載されたもの。

"OR" search(Searchs that contains either of the search keyword)
Connect a search keyword by OR in the text box, or select "OR" in the operator box.
Example: Enter "stomach cancer" OR "gastric cancer".
http://ddbj.nig.ac.jp/arsa/search?lang=en&cond=quick_search&query=%22stomach+cancer%22+OR+%22gastric+cancer%22&operator=AND
The result contains for example,

  • "~ Homo sapiens stomach cancer ~" in the DEFINITION.
  • "~ human gastric cancer ~" in the REFERENCE TITLE.
Example: Enter "stomach cancer" "gastric cancer" into the text box, and select "OR" in the operator box.
http://ddbj.nig.ac.jp/arsa/search?lang=en&cond=quick_search&query=%22stomach+cancer%22+%22gastric+cancer%22&operator=OR
Note:The same results are obtained in the either case.

"NOT" search(Searchs what does not include the keyword after NOT.)
Example: Enter cancer NOT "Homo sapiens"
http://ddbj.nig.ac.jp/arsa/search?lang=en&cond=quick_search&query=cancer+NOT+%22Homo+sapiens%22&operator=AND
The result contains for example,

  • "~ Mouse Cancer Genetics ~" in the COMMENT.

Search that specifies the search field(Searchs that a search keyword is present in the specified field)
There are two ways in this method.

  • Include the search field name in the search keywords.
  • Use the Advanced Search.
The details about the search fieldand Advanced Search are mentioned later.
Note:A search field name and : shold be placed before a search keyword.
Example: Enter Keyword:HTG into the text column.
http://ddbj.nig.ac.jp/arsa/search?lang=en&cond=quick_search&query=Keyword%3AHTG&operator=AND
The result contains for example,

  • "HTG" in the KEYWORDS.
Example: Enter ReferencePubmedID:1111111
http://ddbj.nig.ac.jp/arsa/search?lang=en&cond=quick_search&query=ReferencePubmedID%3A1111111&operator=AND
The result contains for example,

  • "1111111" in the REFERENCE PUBMED.
Example: Enter FeatureQualifier:"CDS /gene=DRB6""
http://ddbj.nig.ac.jp/arsa/search?lang=en&cond=quick_search&query=FeatureQualifier%3A%22CDS+%2Fgene%3DDRB6%22&operator=AND
The result contains for example,

  • "/gene="DRB6"" to FEATURES.

Search by the regular expression
In some search fields, you can use the regular expression in the search keyword.
You should enclose the search keyword in /.
Example: Enter PrimaryAccessionNumber:/AA[1-9]00000/
http://ddbj.nig.ac.jp/arsa/search?lang=en&cond=quick_search&query=PrimaryAccessionNumber%3A%2FAA[1-9]00000%2F&operator=AND
The result contains for example,

  • Like as "AA100000" and "AA900000", top of the numerical part ranges from 1 to 9, at the head of ACCESSION.
    "AA000000" at the head of ACCESSION does not match the search criteria.

Search by the range specification
Search keywords connected by TO are enclosed in [ ].
Example: Enter SequenceLength:[* TO 500],
http://ddbj.nig.ac.jp/arsa/search?lang=en&cond=quick_search&query=SequenceLength%3A[*+TO+500]&operator=AND
The result contains for example,

  • example: Sequence length of LOCUS include the 500 or less.

Advanced Search

Basic search Enter the search keyword to the search box of the field which you want to search.

Example: Enter human into "Definition" column,
The result contains for example, 

  • example: "~ Human parvovirus ~" in DEFINITION.

"OR" search for the single search field Search keywords should be connected by a space.

Example: Enter stomach gastric into "Definition" column,
The result contains for example,

  • example: "~ human gastric lipase ~" toDEFINITION.
  • example: "~ related to stomach cancer ~" to DEFINITION.

"AND" search for the single search fieldEnter the keywords to the search box of the field which you want to search. Keywords are connected by AND.
Example: Enter stomach AND gastric into "Definition" column,
The result contains for example,

  • example: "~ male stomach cDNA ~ polypeptide, gastric specific ~" to DEFINITION.

"OR" search for the plural search fieldsSearch by selecting the OR.

Example:Enter human into "Definition" column, Enter human into "Reference Title" column, and choose "OR" at "Combine Searches with", the result is obtained.
The result contains for example,

  • example: "~ Human metapneumovirus ~" to DEFINITION.
  • example: "~ human cDNA project ~" to REFERENCE TITLE.

"AND" search for the plural search fieldsSearch by selecting the AND

Example:Enter human into "Definition" column, Enterhuman into "Reference Title" column, and choose "AND" at "Combine Searches with", The result is obtained.
  • example: "~ Human glucocerebrosidase ~" to the DEFINITION
  • example: "~ expression of human ~" in the REFERENCE TITLE

Partial match search of Feature/Qualifier Search by Feature Key, Qualifier Name,Qualifier Value.
Example:Enter CDS into "Feature Key" column in "Features",translation into "Qualifier Name" column, and AAA*CC into "Qualifier Value" column,
The result contains for example,

  • example: "/translation="~AAA~CC~"" to CDS of FEATURES.
Example: Enter CDS into "Feature Key" column in "Features", gene into "Qualifier Name" column, and p53 into "Qualifier Value" column,
The result contains for example,

  • example: One which has been described as "/gene="p53"" to CDS of FEATURES.
  • example: One which has been described as "/gene="p53R2"" to CDS of FEATURES.

Details of the search field

Reference: "Available Fields"

"Accession number" in ACCESSION

Search field name Short name regexp search Description Example
PrimaryAccessionNumber pa Yes "Accession number" that is described at the head of
ACCESSION
AB999999
AccessionNumber an Yes AB999999 , AB888888 , AB777777
Division dv Yes "Division" in LOCUS . HUM
SequenceLength sl Yes "Sequence length" in LOCUS . 450
MolecularType mt Yes "Molecular type" in LOCUS . mRNA
MolecularForm mf Yes "Molecular form" in LOCUS . linear
Date dt Yes "Last published date"in LOCUS . 01-JUN-2009
Definition df Yes Text in DEFINITION. Homo sapiens GAPD mRNA for glyceraldehyde-3-phosphate
dehydrogenase, partial cds.
Comment cm Yes Text in COMMENT Human cDNA sequencing project.
Keyword kw Yes Text in KEYWORDS HTC , HTC_FLI , oligo capping
Organism og Yes ORGANISMin ORGANISM Homo sapiens
Lineage ln Yes "Lineage" in ORGANISM Eukaryota , Metazoa , ... , Hominidae , Homo
ReferenceAuthor ra Yes Text in AUTHORSof REFERENCE . Mishima,H. , Shizuoka,T. , Fuji,I.
ReferenceTitle rt Yes Text in TITLE of REFERENCE Direct Submission , Glyceraldehyde-3-phosphate dehydrogenase expressed in human liver
ReferenceJournal rj Yes Text in JOURNAL of REFERENCE Submitted (30-NOV-2008) to the DDBJ/EMBL/GenBank databases.
Contact:Hanako Mishima
National Institute of Genetics, DNA Data Bank of Japan; Yata 1111,
Mishima, Shizuoka 411-8540, Japan
, Unpublished (2009)
ReferencePubmedID rp Yes Text in PUBMED of REFERENCE . 1111111
Feature fe Yes "Text of Feature" in FEATURES
source 1..450
/chromosome="12" 
/clone="GT200015" 
/clone_lib="lambda gt11 human liver cDNA (GeneTech.
No.20)" 
/db_xref="taxon:9606" 
/map="12p13" 
/mol_type="mRNA" 
/organism="Homo sapiens" 
/tissue_type="liver"
CDS 86..>450
/codon_start=1
/gene="GAPD" 
/product="glyceraldehyde-3-phosphate dehydrogenase" 
/protein_id="BAA12345.1" 
/transl_table=1
/translation="MAKIKIGINGFGRIGRLVARVALQSDDVELVAVNDPFITTDYMT
YMFKYDTVHGQWKHHEVKVKDSKTLLFGEKEVTVFGCRNPKEIPWGETSAEFVVEYTG
VFTDKDKAVAQLKGGAKKV" 
FeatureQualifier fq Yes "Text of Qualifier" in FEATURES
source 1..450
source /chromosome=12
CDS /translation=MAKIKIGINGFGRIGRLVARVALQSDDVELVAVNDPFITTDYMT
YMFKYDTVHGQWKHHEVKVKDSKTLLFGEKEVTVFGCRNPKEIPWGETSAEFVVEYTG
VFTDKDKAVAQLKGGAKKV
AllText at - Full text that is described in the flat file. LOCUS//
 
LOCUS       AB000000              450 bp    mRNA    linear   HUM 01-JUN-2009
DEFINITION  Homo sapiens GAPD mRNA for glyceraldehyde-3-phosphate
            dehydrogenase, partial cds.
ACCESSION   AB999999 AB888888 AB777777
VERSION     AB000000.1
KEYWORDS    HTC; HTC_FLI; oligo capping.
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 450)
  AUTHORS   Mishima,H. and Shizuoka,T.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-NOV-2008) to the DDBJ/EMBL/GenBank databases.
            Contact:Hanako Mishima
            National Institute of Genetics, DNA Data Bank of Japan; Yata 1111,
            Mishima, Shizuoka 411-8540, Japan
   PUBMED   1111111
REFERENCE   2
  AUTHORS   Mishima,H., Shizuoka,T. and Fuji,I.
  TITLE     Glyceraldehyde-3-phosphate dehydrogenase expressed in human liver
  JOURNAL   Unpublished (2009)
COMMENT     Human cDNA sequencing project.
FEATURES             Location/Qualifiers
     source          1..450
                     /chromosome="12" 
                     /clone="GT200015" 
                     /clone_lib="lambda gt11 human liver cDNA (GeneTech.
                     No.20)" 
                     /db_xref="taxon:9606" 
                     /map="12p13" 
                     /mol_type="mRNA" 
                     /organism="Homo sapiens" 
                     /tissue_type="liver" 
     CDS             86..>450
                     /codon_start=1
                     /gene="GAPD" 
                     /product="glyceraldehyde-3-phosphate dehydrogenase" 
                     /protein_id="BAA12345.1" 
                     /transl_table=1
                     /translation="MAKIKIGINGFGRIGRLVARVALQSDDVELVAVNDPFITTDYMT
                     YMFKYDTVHGQWKHHEVKVKDSKTLLFGEKEVTVFGCRNPKEIPWGETSAEFVVEYTG
                     VFTDKDKAVAQLKGGAKKV" 
BASE COUNT          102 a          119 c          131 g           98 t
ORIGIN
        1 cccacgcgtc cggtcgcatc gcacttgtag ctctcgaccc ccgcatctca tccctcctct
       61 cgcttagttc agatcgaaat cgcaaatggc gaagattaag atcgggatca atgggttcgg
      121 gaggatcggg aggctcgtgg ccagggtggc cctgcagagc gacgacgtcg agctcgtcgc
      181 cgtcaacgac cccttcatca ccaccgacta catgacatac atgttcaagt atgacactgt
      241 gcacggccag tggaagcatc atgaggttaa ggtgaaggac tccaagaccc ttctcttcgg
      301 tgagaaggag gtcaccgtgt tcggctgcag gaaccctaag gagatcccat ggggtgagac
      361 tagcgctgag tttgttgtgg agtacactgg tgttttcact gacaaggaca aggccgttgc
      421 tcaacttaag ggtggtgcta agaaggtctg
//

Format of the search keyword

Specification of the search field
  • (Search field name or Short name) + ':' + (Search keyword)

Boolean operator ("AND", "OR", "NOT" search)
  • (Search keyword) + ' AND ' + (Search keyword)
    (Search keyword) + ' && ' + (Search keyword)
    (Search keyword) + ' +' + (Search keyword)
  • (Search keyword) + ' OR ' + (Search keyword)
    (Search keyword) + ' || ' + (Search keyword)
  • (Search keyword) + ' NOT ' + (Search keyword)
    (Search keyword) + ' -' + (Search keyword)

Grouping
  • '(' + (Search keyword) + (Logical operator) + (Search keyword) + ')'

Range search
  • (Search field name or Short name) + ':[' + (Start value or '*') + ' TO ' + (End value or '*') + ']'
    Including start value, end value
  • (Search field name or Short name) + ':{' + (Start value or '*') + ' TO ' + (End value or '*') + '}'
    Not including start value, end value

Wild card search
  • (Search keyword) + '*'
  • '*' + (Search keyword)
  • (Search keyword) + '*' + (Search keyword)
    '*' matches any texts more than 0 characters
  • (Search keyword) + '?' + (Search keyword)
    '?' match in any one character

Phrase search
Search in sequence the search keyword. Or search characters that have special meaning.
  • "' + (Search keyword) + '"'

Regular expression search
  • '/' + (Search keyword) + '/'
Example of the regular expression
  • . (any single character)
    example : /Homini.ae/ matches the for example 'Hominidae' and 'Homininae'.
  • * (a letter more than 0)
    example : /AB0*/ matches the for example 'AB', 'AB0', 'AB00', 'AB000'
  • .* (zero or more of the preceding element)
    example : /AB.*/ matches the for example 'AB', 'AB0', 'AB789' , 'ABXYZ'
  • ? (Previous character is 0 or 1)
    example : /AB?00000/ matches 'AB000000' and 'A000000'
  • + (Previous character is 1 or more)
    example : /AB0*/ matches the for example 'AB0', 'AB00', 'AB000' , but does not match 'AB'
  • [abc] (character 'a' , 'b' or 'c')
    example : /Homini[dn]ae/ matches 'Hominidae' and 'Homininae'
  • [^abc] (except character 'a' , 'b' , 'c')
    example : /Homini[^d]ae/ matches 'Homininae' but does not match 'Hominidae'
  • [a-z0-9] (character 'a' ~ 'z' or '0' ~ '9')
    example : /AA[0-9]00000/ matches the for example 'AA100000'
  • { n } (Previous character occurs n times exactly)
    example : /AB0{2}/ matches 'AB00' but does not match 'AB0' and 'AB000'
  • { n ,} (Previous character occurs n times or more)
    example : /AB0{2,}/ matches the for example 'AB00' , 'AB000' , but does not match 'AB0'
  • { n , m } (Previous character occurs at least n and not more than m times
    example : /AB0{2,4}/ matches the for example 'AB00' , 'AB0000' but does not match 'AB0' and 'AB00000'

Fuzzy Search
Search for a word of spelling similar to the search keyword
  • ':' + (Search keyword) + '~' + (Distance of the search term. Numerical value of 0.0 or more and less than 1.0. Close to the search keyword closer to 1.)

Proximity Search
The words contained in a phrase search what is indicated in the neighborhood.
  • ':' + (Phrase) + '~' + (Distance of the search term. Number of words.)

Weighting Search

  • (Search keyword) + '^' + (Positive relative weight. Positive number. Default is 1.0.)

Character with a special meaning
These characters have a special meaning.
+ - && || ! ( ) { } [ ] ^ " ~ * ? : /
When you search these characters, use phrase search, or cancel the special meaning by prefixing the ''\''

Get the search results (view/download)

Your results are available in the following formats.

FlatFile DDBJ FlatFile format
FASTA FASTA format
XML INSD-XML format
In the browser
  • Click the Accession number which you would like to view the content. You can view the Flatfile of the entry.
  • Specify the format. Check the results you want to view, and click the "View selected" button. You can view the results that was selected in the specified format. (1,000,000 upper limit)
  • >

  • When your result is over the upper limit, refine your search condition.

Download
  • To download results, specify the format and click the "Download All" button (1,000,000 upper limit).
  • To download the selected files, specify the format and check the box you want to download. Then click the "Download selected" button (1,000,000 upper limit).
  • (Caution)In case of downloading XML formated file, if there are a large number of entries, multiple XML declaration lines are included in one file. Please divide the file and/or check the start line as appropriate.

Filter the search results
If you click the "Facet", you can filter your search results by the following condition.
Kind of filters
  • Division
  • Organism

"Search Settints" of "Advanced Search".

Specifiction of the following seach conditions are also available at the "Search Settints" of "Advanced Search".

Sort condition
You can select a search field or search score for sorting.
Display field of the search results
Check the box(es) you want to display on the search results.
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