Last updated:2017.5.30.

What is MSS? – Mass Submission System

Before your data submission, please confirm Categories for Sequence Data. If you are to submit raw outputs from sequencers, please read DRA; DDBJ Sequence Read Archive and DTA; DDBJ Trace Archive.

Submission of research data from human subjects
For all data from human subjects researches submitted to DDBJ, it is submitter's responsibility to ensure that the dignity and the right of participant (human subject) is protected in accordance with all applicable laws, regulations and policies of submitter's institute.
In principle, make sure to remove any direct personal identifiers of human subjects from your submissions.
Before submission, read "Submission of research data from human subjects".

We at DDBJ recommend using Mass Submission System (MSS) when:

Nucleotide Sequence Submission System is an interactive application to enter all of items required for your submission on step by step basis. When the submission contents are not so many, Nucleotide Sequence Submission System is very useful, an easy procedure for your submission. However, in case of large scale submission, such as thousands of ESTs, it is more useful to send submission files directly to DDBJ, rather than Nucleotide Sequence Submission System

MSS is a procedure for large scale submission.

Before using MSS

Before sending your data to DDBJ, please apply from MSS application form.
Then, DDBJ will introduce MSS manuals and software tools to help your submission.


Submission files required for MSS

For using MSS, following two files are basically required;

Sequence file

The text file that contains all nucleotide sequences in FASTA format.

Annotation file

The tab delimited text file that contains your data other than sequences, such as submitters, references and biological features.

  • Submitters are supposed to prepare the two files to submit their data.
    You can make the files with some scripts, spread sheets (such as MS Excel), text editors and so on.
  • Before submitting to DDBJ, the files should be checked with software tools provided from DDBJ, named UME (Utilities for MSS Error check) or Parser / transChecker.
  • Please refer to each manual to use the software tool.
    You can get the tools and their manuals on MSS home
    See also End-user license agreement carefully before using the tools.
  • When you have to describe protein coding sequences for annotation of your sequence, the annotation file containing CDS feature(s) as biological features should be checked with UME or transChecker tool before submitting to DDBJ.


The Flowchart of MSS



Please apply for your submission from MSS application form.
Or, please contact to ad_mass if you need preliminary consultation.


2.Test submission

Please make samples for both of sequence and annotation files with some of your entries.
Then, please send them to DDBJ by e-mail or file transfer.
If the total size of files is more than 10 M bytes, we recommend you to use file transfer by SCP using public/private key pair.

Before sending the files, please check them with UME or Parser / transChecker tool and fix error(s) in your files if there is any error.


3.Check for test submission

The test data will be validated in accordance with an international rule agreed with DDBJ/EMBL-Bank/GenBank and DDBJ rule.
We ask you to revise the files, if necessary.



Please make both of sequence and annotation files in correct format including all data and check them by UME or Parser / transChecker tool.

Then, please send them to DDBJ by e-mail or file transfer.
If the total size of files is more than 10 M bytes, we recommend you to use file transfer by SCP using public/private key pair.


5.Check for all submission

We will review the data. We ask you to revise the files, if necessary


6. Assign and acknowledge Accession number(s)

We will inform accession numbers for your data to the 'Contact Person' by e-mail.


7. Data release or hold

If you do not set any hold-date, your data will be released immediately.
When you set a hold-date for your data, we will release your data according to Principle of "Hold-Until-Published" data release

Based on your sequence and annotation files, your data will be processed and publicized into the DDBJ format, so called "flat file".
See also relationships between annotation file and DDBJ flat file.


File transfer: Upload your files to our server via D-Way

Before using the file server, you need D-way login account.
Please visit DDBJ Submission Portal D-way to get D-way login account and to upload files.
For detail, see an introduction for uploading files and generating key pair on Submission Account.

You can find tutorials at Upload sequence data.
See also video tutorials on DDBJ Movies.

  • Generate key pair (Windows)
  • Generate key pair (Mac)
    Notice: The "public key" file can be uploaded on "Account" page after you login on D-way.
    Do not sent DDBJ the “public key” file by email.
  • Upload data files (Windows)
  • Upload data files (Mac)
    Notice: Although title of each movie says "Submission to DRA", the procedure to upload submission files for MSS is basically in the same way.