Last updated:2014.12.17.

Nucleotide Sequence Submission

It is now the usual practice for authors to acquire accession numbers to their sequences when they submit articles to journals. DDBJ is here for the author and the journal. DDBJ is also ready to assign accession numbers to sequences even if any publication is neither accompanied nor expected. The data archived in the International Nucleotide Sequence Databases by DDBJ will be diffused to the public by DDBJ, EMBL-Bank/EBI and GenBank/NCBI, and other data distributors. Thus, DDBJ is here for users as well.

If you are to submit not only nucleotide sequence data but also raw outputs from sequencers, please read DRA; DDBJ Sequence Read Archive and DTA; DDBJ Trace Archive.

It would make your submission quick and clean, if you could read the following document in advance:

Required items for nucleotide sequence submission

Please prepare neat lists of the following items before your submission.

Submitters

The items, affiliation, postal address, phone and fax numbers of contact person and all names of submitters are required. Some of those items will be indicated in REFERENCE 1 on the flat files of the entries. After 2008, none of E-mail address, phone or fax number of the contact person is displayed without disclosing request from submitters.

Notice 1: Submitter should not be only one person.
Submitter of the entry is the person who have responsibility to the submitted data in the entry. We accept updating requests only from the original submitter of the entry.
Basically, we strongly recommend to describe joint submitters more than two persons, e.g. at least a true worker and an adviser, to avoid lost communication in future.
In principle, we cannot accept any sequence data from a student without whose advisers in names of submitter.

Notice 2: let us know your FAX number
Generally, DDBJ contacts submitters via E-mail. However, in case of breakdown of communication via E-mail by any reason, DDBJ would contact submitters via fax.
So, please let us know your fax number, if possible.

Date of data release to the public

Submitters can select the status of their data, either "immediately release" or "hold until published". "hold date" is the date to start the distribution of the entry. Submitter can specify the date, if necessary
If you selected "hold until published", it is required to specify the "hold date" of your data.
Reference: Principle of "Hold-Until-Published" data release

Number of sequences

If you would like to have consecutive accession numbers, you should fix the number of entries before your submission.

Even if your sequence is identical to previously reported sequence(s), on the condition that the sequence is independently determined, you can submit it as a "new" entry. Basically, DDBJ accepts all sequence data that are independently determined, even though sequences are identical each other.
However, for variation studies, DDBJ also accepts submissions of multiple identical sequences with frequency and total sample number. DDBJ recommends to normalize research data for variation studies by appropriate set of entries; basically, the number of entries should be equal to multiplication of numbers of sequence polymorphisms and sampled populations.
See also representative submissions of identical sequences for variation studies, in detail.

Scientific paper, REFERENCE

You have to describe authors and title of the main paper for the sequence, as a primary citation. Even though you have no plan to submit any paper for you sequence, please enter authors and title, formally.

You can describe just referred papers which does not describe about the submitting sequence, if necessary.

Biological knowledge related to nucleotide sequence

Whether the species is identified or not, it is required to describe the relevant information on the biological origin of your sequence with organism name etc.

As annotation for your sequence, features should be described, if at all possible. You should describe features such as protein coding sequences (CDS), rRNAs, tRNAs, ncRNAs and so on with their locations. Please also describe qualifiers, such as product, gene and so on, arbitrarily.

Notice: protein coding sequence; CDS feature should have gene and product.
See also the guideline of gene nomenclature at DDBJ before your submission.

Nucleotide sequences

You can use IUPAC nucleotide base codes to describe your nucleotide sequences.

In general, you have to exclude following sequences from your data, except that you are to submit an artificially constructed sequence such as expression vector, etc.

  • The sequence derived from a vector.
  • The sequence derived from a linker and/or an adapter.
  • The sequence derived from primer that is designed by referring from the highly conserved region of which the real sequence is unknown.

Before your submission, we strongly recommend you to screen your sequences with our web service; VecScreen.

 

Workflow of the data submission to DDBJ

See also Sequence Data Transition.

1 Data Submission

(A) Nucleotide Sequence Submission System
DDBJ generally recommends you to use Nucleotide Sequence Submission System.
(B) Mass Submission System(MSS)
We recommend the use of the Mass Submission System (MSS) if:
(1) the submission consists of large number of sequences (entries); greater than 1024,
(2) the submission involves long (greater than 500 kb) nucleotide sequences which result in a complex submission containing many features (greater than 30 in an entry) as in the case of genome data, or
(3) the submission cannot be handled by Nucleotide Sequence Submission System.

Please go to the Mass Submission System(MSS) for details.

2 Annotation

We annotate in accordance with our rules and the international rules agreed upon by the DDBJ/EMBL-Bank/GenBank consortium. In the annotation process, we may contact the Contact Person to make inquiry about the data.

3 Assignment and Notification of Accession Number

We e-mail an accession number (unique number assigned by the International Nucleotide Sequence Database Collaboration) to the Contact Person whose E-mail address is entered in the "Contact person E-mail address" field.
This notification is normally sent within five business days after receipt of the data.
If you do not hear from us within this time period, please contact us.

4 Report of Data Releasing

We notify data release to the Contact Person by E-mail or FAX. Once the data are released, please confirm the data by one of the retrieval tools accessible from the DDBJ homepage (e.g., getentry).

If you would like to update your data, please send a request mail to ddbjupdtwith the necessary information. Please refer to Updates/Correction (after getting your accession number) for details.

5 General Information

For general inquiry on DDBJ
For data submission
For updating submitted data
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