FAQ

Previous versions of sequence data are available by using getentry webAPI.

See gethistory on getentry HELP.

When you kindly describe about using DDBJ on academic papers etc., in general, please use the latest article for DDBJ on Nucleic Acids Res. Database issue as a reference.

However, please note followings.

In case of citation for each sequence record

In general, it is enough to describe accession number for it in your publication.
If you discuss about the data in detail, please use primary citation for the data as a reference.

In case of citation for each service provided at DDBJ

In general, please use original article for each service as a reference.

References:

We would like to acknowledge DDBJ in our publication.

We would like to acknowledge the NIG Supercomputer System in our publication.

Since 2007, we have removed E-mail addresses and phone numbers from sequence data.
If you can find a related paper at REFERENCE on DDBJ flat file, contact information would be available on the paper.
When you wishes to contact to the submitter(s) of an entry of your interest, please contact us via Inquiry to the sequence submitters (submitted to DDBJ) with reasons briefly, then we will forward your message to the submitter(s).

In general, see the rule of the journal (i.e. Instructions to Authors), and follow it.
At INSDC, we recommend you to describe accession numbers in the footnote on the title page of your paper as following;
Note: Nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession number(s)----'.

It is the date of the last release of the data. See LOCUS of Explanation of DDBJ flat file format.

It indicates that this data is directly submitted from the submitter. The term is the antonym to "journal scan".
REFERENCE 1 is the information of submitter(s), not general reference.
So, do not describe "Direct Submission" in the title for literature in REFERENCE 2 or after.

See followings.

• The DDBJ/EMBL/GenBank Feature Table Definition
• Definition of Feature Key
• Definition of Qualifier Key
• Example of Submission
• Feature/Qualifier Usage Matrix

In general, you can find accept date in JOURNAL line of REFERENCE 1 on DDBJ flat file.
Please note that some old data do not have the description of accept date.

See Principle of “Hold-Until-Published” data release and Overview of International Nucleotide Sequence Databases Policies.

There are some possibilities as followings.

1) In case of the meantime of data distribution:

The data may be on the process of data distribution. If you are unable to retrieve the data longer than a week, please send an inquiry including the accession number to

2) The specified hold date of the data is in holidays of DDBJ:

We will release the data after holidays of DDBJ. See also DDBJ Calender.

3) In case of not yet confirmed the accession number is published on a paper or others:

Please let us know the paper or other media in which the accession number is described.

4) In case of the data submitted BEFORE January 1, 1998:

The sequence data be still unpublished after hold date.

In case of 3) or 4), we will check and support it.
Please contact us from contact form by selecting the item, "Updating Submitted Data" with accession numbers, or by mail to.

References

Principle of "Hold-Until-Published" data release

Can not find the sequence data, though the accession number cited on a paper.

For once published entries, we can restrict to use the data, if the conditions are right.
In case of the restriction, DDBJ will not include the data in its periodical release and remove from all services under DDBJ.
However, the data is permanently available on getentry queried with its accession number.
# The rule is not applied, when the data is published by any mistake of INSD.
This policy is written in the document prepared by International Advisory Committee of INSD on Overview of International Nucleotide Sequence Databases Policies as follows;

All database records submitted to the INSD will remain an entry accessible as part of the scientific record. Corrections of errors and update of the records by authors are welcome and erroneous records may be removed from the next database release, but all will remain permanently accessible by accession number.

In addition, there are a number of databases constructed by occasionally using data from INSD.
DDBJ can not support to delete data from such databases. If you are to delete the cited data on other databases, you have to contact managing staff of each database, directly.

Reference

INSDC Status Document

DDBJ releases sequence data submitted with a hold date according to Principle of “Hold-Until-Published” data release.

Please confirm if the ID on the paper is Accession Number Assigned by INSD or not.

If accession numbers on the paper, please contact us from contact form by selecting the item, "Updating Submitted Data" with following items.

• Accession numbers on the paper
• Title of the paper
• Authors
• Journal name
• Volume, pages, year
• DOI, PubMed ID, URL

It is getentry.
"getentry" is a system for data retrieval by accession numbers, etc.
In general, the sequence data will be available on getentry from the day after processed to release.

DDBJ is functioning as one of the international nucleotide sequence databases, including EMBL-Bank/EBI in Europe and GenBank/NCBI in the USA as the two other members.
When DDBJ releases the submitted data, EMBL-Bank and GenBank will load the data into their own services, respectively.
See Sequence Data Transition.
Note that the data are converted into EMBL-Bank or GenBank format.

In general, the data released from EMBL-Bank or GenBank are loaded into DDBJ services and published from DDBJ within their released date.
The data released from DDBJ are loaded into ENA/EBI and GenBank and published from them within a few days.
However, the data release processes at all three databases may be delayed, because of system maintenance, troubles on the network, or any other reasons. So, we can not specify the temporal differences among them.

The rule to translate nucleotide sequence into amino acid sequence is specified in accordance with agreements of International Nucleotide Sequence Database Collaboration.
The codon table using a CDS feature is specified in the value of /transl_table qualifier as a number of The Genetic Codes.

There are three points frequently misunderstood.

• You should specify /organelle qualifier to assign correct genetic code for mitochondrion or chloroplast.
• The initiation codon is M, Met, methyonine, not G or V.
      See Start codon and N-Formylmethionine
• When an amino acid can be specified by two bases (i.e. degeneracy of codons), it will be outputted.

There are some exceptional cases, represented by RNA editing and so on.

INSD; International Nucleotide Sequence Database are composed of DDBJ, ENA and NCBI, and collect experimentally determined nucleotide sequence data.
A unique accession number issued by INSD for each submitted sequence data is defined as the INSD accession number.
On DDBJ flat file, the accession number is described in ACCESSION line.

If multiple entries are united to an entry, or if an entry is extensively modified after the submission, the responsible data banks may assign a new accession number to it. In these cases, the new accession number is called the primary accession number, and the old accession number(s) is/are called the secondary accession number(s).

In the flat file, the primary accession number is indicated first, then the secondary accession number(s) follows.

example
ACCESSION   AB999999 AB888888 AB777777

AB999999 -- primary accession number

AB888888 AB777777 -- secondary accession number

You can find the same updated entry with both the primary and the secondary accession numbers, in general.
However, if the old entry with secondary accession number has previously been open to the public, the old one is not removed. So, you can find the old record by getentry.

References

getentry HELP

INSDC Status Document: Replaced

Why is the retracted data still available?

• The name of the search program and/or the URL that you used to conduct the search.
• The search conditions that you used.
• The date and time at which you conducted the search.
• Accession number of the entry that should have been found.
• URL of the search results.
• Any other relevant information.

• Can not find the sequence data, though the accession number cited on a paper.
• I am having trouble finding an accession number that should be publicly available.

• Conducting searches and analyses using a network server such as an FTP or web server.
  You may access these networking tools via Search / Analysis. 　
• Conducting searches and analyses by logging in to the supercomputer system at the National Institute of Genetics (NIG).
  (This requires a supercomputer user ID. You will need to sign up for a new user account on the NIG supercomputer system.)

Search results may be accessed via the following URL, which contains a Request ID field.

http://blast.ddbj.nig.ac.jp/blast/r/Request ID

Request ID

Note that the Request ID will be displayed in the window that appears after transmitting the input. Make sure to note down this.

Input content post-transmission window

Search results display window

Reading period

Search results may be viewed up to 7 days after the execution of the search.

1. Precedence table of sequences with high homology scores
2. Homologous sequences and their alignment
3. Parameters and statistics

DDBJ HP

OS：Windows7 or later , Mac OSX10.9 or later

Browser：Firefox latest versions , Chrome latest versions

DDBJ Nucleotide Sequence Submission System

Browser：Firefox , Chrome

D-way Submission System

Browser：Firefox latest version, Chrome latest version

BLAST / ARSA

OS：Windows7 or later , Mac OSX10.6 or later

Browser：IE10.X , IE9.X , Firefox , Chrome , Safari5.X or later

To get a FASTA format of TSA or WGS entries, please use "getentry", specifying the following values.

 ID : Specify the Accession Number.
 Output format : Select "total nt seq FASTA" for the result.
 Result : Select one from the following filetype for the output.

• html
• text
• compress (gz)

For more information about each value, please see getenry HELP.

Please see the following video as well.

The activity of the NIG Supercomputer System are evaluated by the acknowledgments of all of you.
Please acknowledge in your papers, presentations and other publications, the role of NIG Supercomputer System played in your research.
It is no problem to modify the following example for the connection of sentences.

Computations were partially performed on the NIG supercomputer at ROIS National Institute of Genetics.

When you use DDBJ services in your research, we would appreciate it if you would include a reference to DDBJ in your publications.
If you consider citation of DDBJ paper is unsuitable, please consider to acknowledge in your publications, the role of DDBJ services played in your research.
It is no problem to modify the following example for the connection of sentences.

This research was performed using "name of DDBJ Service, analytical tools".