ARSA

Searchable DataBases

ARSA retrieves the following databases.

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: Example: Enter lung cancer to the text box, and select “AND” as a boolean operator.

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 Hom*.

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”

The result contains for example,
“~ Human lung cancer associated ~” in the DEFINITION.

“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.

The same results are obtained in the either case.

Example: Enter “stomach cancer” OR “gastric cancer”

Example: Enter “stomach cancer” “gastric cancer” into the text box, and select “OR” in the operator box.

”~ Homo sapiens stomach cancer ~” in the DEFINITION
“~ human gastric cancer ~” in the REFERENCE TITLE

“NOT” search（Searchs what does not include the keyword after NOT.)

Example: Enter cancer NOT “Homo sapiens”.

The result contains for example,
“~ Mouse Cancer Genetics ~” in the COMMENT.

Search that specifies the search fiel（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.

The result contains for example,
“HTG” in the KEYWORDS

Example: Enter ReferencePubmedID:1111111

The result contains for example,
“1111111” in the REFERENCE PUBMED

Example: Enter FeatureQualifier:”CDS /gene=DRB6”

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/

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].

The result contains for example,
Sequence length of LOCUS include the 500 or less.

Advanced Search

Basic searchEnter 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,　
“~ Human parvovirus ~” in DEFINITION

“OR” search for the single search fieldSearch keywords should be connected by a space.

Example: Enter stomach gastric into “Definition” column,

The result contains for example,
“~ human gastric lipase ~” to DEFINITION “~ 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,
“~ 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,
“~ Human metapneumovirus ~” to DEFINITION “~ human cDNA project ~” to REFERENCE

“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.

The result contains for example,
“~ Human glucocerebrosidase ~” to the DEFINITION “~ expression of human ~” in the REFERENCE TITLE

Partial match search of Feature/QualifierSearch by Feature Key, Qualifier Name,Qualifier Value.

Example: Enter CDS into “Feature Key” column in “Features”, translation “Qualifier Name” column, and AAA*CC into “Qualifier Value” column,

The result contains for example,
“/translation=”～AAA～CC～”” to CDS of FEATURES

Example: Enter CDS into “Feature Key” column in “Features”,gene “Qualifier Name” column, and p53 into “Qualifier Value” column,

The result contains for example,
One which has been described as “/gene=”p53”” to CDS of FEATURES One which has been described as “/gene=”p53R2”” to CDS of FEATURES

Details of the search field

Reference: ‘Available Fields’

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" 

source 1..450
source /chromosome=12
CDS /translation=MAKIKIGINGFGRIGRLVARVALQSDDVELVAVNDPFITTDYMT
YMFKYDTVHGQWKHHEVKVKDSKTLLFGEKEVTVFGCRNPKEIPWGETSAEFVVEYTG
VFTDKDKAVAQLKGGAKKV

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

Your results are available in the following formats.

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. (10,000 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 (Downloadable entries, 3,000 at most).

To download the selected files, specify the format and check the box you want to download. Then click the “Download selected” button.

[Caution]

• For download all the results without fail, you should reduce the total number of the results less than 3,000 at most. The number of downloadable entries might be decreased because it depends on the load status of the server. You can reduce the number of the results by adding the date filter.

  　　Advanced Search     Date  20180101 to 20180630
  　　Quick Search        Date:[20180101 TO 20180630]
  

• 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

Other search criteria

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.