Nucleotide Sequence Submission
Before Nucleotide Sequence Submission
Purpose and Significance of Nucleotide Sequence Submission
In many scientific journals, it is required to assign and to describe INSDC accession number for a nucleotide sequence on the research paper. DDBJ is a member of International Nucleotide Sequence Database Collaboration (INSDC).
When you wish to publicize your sequence through DDBJ, and your sequence is acceptable for DDBJ, you can submit your sequence to DDBJ, even if you have no plan to publication of any research paper related to the sequence.
Once released, the nucleotide sequences submitted to INSDC including DDBJ are available for everyone.
If you submit nucleotide sequences to DDBJ, you can get NO priority for patent.
New Submission or Update?
When you wonder your sequence data should be newly submitted or your previous entry should be modified, do not hesitate to contact us at Contact form "Data updates / Corrections".
Nucleotide Sequence Submission System is a tool only for new submission, so, do not use Nucleotide Sequence Submission System to send your update request. If you need to modify your previous entry, see the link for update request, and contact us at Application Form for Data Update Requests.
Rights and Duties of Submitter
For sequence submission to DDBJ, it is required for submitters to provide not only nucleotide sequence but also address of submitters and contact person, reference(s) (including primary citation), names of source organisms, function, natures of genes, and so on (collectively means "registration information" of the entry).
Following the progress of research, personnel change, and/or correction of some error, submitters of the entry can revise and/or update their own nucleotide sequence and registration information.
As mentioned above and the page to explain dataflow, the nucleotide sequences released from DDBJ are available for everyone. When a user other than the submitter of the entry points out some error(s) in the entry, DDBJ will inform it to contact person of the entry. Since only submitters of the entry can revise and/or update the entry, it depends on the submitters of the entry if the entry is modified following user's claim or not.
Basically, it is required for the submitters to response user's inquiry about their own entry. When you wish to contact to the submitter(s) of an entry of your interest, please contact us through the inquiry form with reasons briefly, then we will forward your message to the submitter(s). So, do not block E-mails from DDBJ.
When there is a disagreement between users and submitters on registration information of an entry, DDBJ maintains neutrality for both opinions.
Releases of Primary Citation and Sequence Data
During preparation/submission of primary citation, DDBJ can store your registration information privately in the meantime. If necessary, submitters have to include a hold date in their registration information. Then, the entry with a hold date is stored privately at DDBJ. DDBJ must maintain registration information as confidential until publication of the entry.
The hold data will be open to the public according to principle of data release.
In principle, even submitters cannot remove their own entry if the entry has already been released and/or the accession number is publicized in Journal etc.
However, DDBJ can suppress the entry in many of its services following the submitter's request.
Required items for nucleotide sequence submission
The items, affiliation, postal address and phone number of contact person and all names of submitters 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.
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, feature should be described, if at all possible. You should describe features such as protein coding sequences (CDS), rRNA, tRNA, ncRNA and so on with their location. Please also describe qualifiers, such as product, gene and so on, arbitrarily.
You can use IUPAC nucleotide base codes to describe your nucleotide sequences.
Before your submission, we strongly recommend you to screen your sequences with our web service;VecScreen.
Workflow of the data submission to DDBJ
1 Data Submission
We annotate in accordance with our rules and the international rules agreed upon by the DDBJ/ENA/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 inform 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. 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 from Application Form for Data Update Requests with the necessary information. Please refer to Updates/Correction (after getting your accession number) for details.
5 General Information
Sequence Data Transition
Following figure shows the dataflow from new submission to release and update at DDBJ.