Last updated:2014.7.3.


Keyword Search

Tag Search(NSSS:DDBJ Nucleotide Sequence Submission System , MSS:Mass Submission System)

FAQs 19 : Tag = mss-submission
How to submit sequence data with annotation to DDBJ? category format MSS NSSS submission

Select from following two ways.

In general, we recommend to use DDBJ Nucleotide Sequence Submission System
In cases of, large number of sequences, many features, and/or long sequences, MSS is more useful.

Last Updated:June 16, 2014
How to describe organism name, if the species is not identified or not defined? format MSS NSSS submission
Last Updated:June 16, 2014
How to submit sequence data directly obtained from soil or sea water? format MSS NSSS submission

In cases of sequences derived by direct molecular isolation from soil, sea water, etc. i.e. a bulk environmental DNA sample by PCR with or without subsequent cloning of the product, DGGE, or other anonymous methods, see What is ENV ? – environmental samples.
For description of organism qualifier, see 3. Environmental samples.

Though frequently confused, the term, 'environmental samples', does NOT mean "wild type". If sequences are derived from isolated or cultured organisms, the sequence data are not classified into environmental samples.

Last Updated:June 16, 2014
How to describe organism name for artificially constructed sequence? format MSS NSSS submission
Last Updated:June 16, 2014
How to descrbe the evidence of speculation for the feature? format MSS NSSS submission

You can use experiment or inference qualifier to describe evidence of speculation in each feature.

Last Updated:June 16, 2014
Can I submit seuqence data without any published paper, during writing or in press? MSS NSSS submission

Yes you can. It ought to be required at 'instructions to authors' of most of journals to submit sequence data to DDBJ (, EMBL-Bank or GanBank) before the paper submission.
During submission of sequence data, select status for your REFERENCE as follows.

  • "Unpublished"; In cases of preparing paper, during paper submission, or you do not prepare any publication.
  • "In Press"; When your paper is accepted and in press.

Your citations will be appeared at REFERENCE 2 or after on DDBJ flat file.

Last Updated:June 19, 2014
When we have no plan to paper publication, how to describe REFERENCE? format MSS NSSS submission

Regardless you are to publish academic paper or not, DDBJ accepts your submission of sequence data.
If you have no plan to paper publication, you have to fill following items of REFERENCE.

  • status: [Unpublished]
  • year: tentative year (this year), i.e. 2014
  • title: tentative title to explain your data
  • ab_name (authors): abbreviation of tentative author(s) (often the same as ab_name of SUBMITTER)

When you change your plan after sequence data submission, i.e. if you publish a paper, contact us from this form to send request with subject "Our paper was published".

Last Updated:June 16, 2017
Is it OK to submit sequence data by only one submitter? format MSS NSSS submission

DDBJ accepts 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.

See Required items for nucleotide sequence submission.

Last Updated:June 19, 2014
In a circular genome, when a feature is located in the base range joined from the last base to the first base, how to describe the location of the feature? format MSS NSSS submission

For instance, when the length of sequence is 199035 bp and a CDS feature is located in the range from 199001 to 100, you should describe the location of CDS feature as
See also Description of Location in detail.

Last Updated:June 30, 2014
To submit a complete sequence of a genome, are annotation data for the genome required? format MSS submission

As feature annotation, we strongly recommend you to describe CDS (protein-coding sequence)rRNAtRNA and so on.
Please inform us in detail, when you apply to Mass Submission System.

Last Updated:June 15, 2017
How to describe a submiter or an author who has first name only? format MSS NSSS submission
In case of Mass Submission System
Describe first name, only.
Though some warning will be outputted, please ignore them.
In case of Nucleotide Sequence Submission System
Please enter first name with some dummy initial.
Please inform us about the person with "Submission Information" on final page.
Last Updated:November 27, 2017
Can not find appropriate feature key MSS NSSS submission

See Definition of Feature Key and Feature Table Definition.
When you can not find any accommodated feature, use misc_feature and enter information in value of /note qualifier.

For instance, since DDBJ is a database for nucleotide sequences, we do not prepare any specific item for amino acid sequence motifs.
However, you can describe such kind of information by using misc_feature with /note qualifier.

Last Updated:June 9, 2014
How can I input amino acid sequence (/translation qualifier) for CDS feature? format MSS NSSS submission

The amino acid sequence for CDS feature will be automatically translated from nucleotide sequence according to location and other items, and reflected into /translation qualifier. So, in general, do not enter it.

[Nucleotide Sequence Submission System] How to confirm translated amino acid sequences (i.e. /translation qualifier) for CDS features?
The amino acid sequence in the value of /translation qualifier seems to be incorrect.
Last Updated:July 7, 2014
Which should I use to submit to DDBJ, Nucleotide Sequence Submission System or Mass Submission System? MSS NSSS submission

Nucleotide Sequence Submission System is an interactive application to enter all of items required for your submission on step by step basis.
To use Mass Submission System (MSS), submitters have to make submission files by themselves. So, DDBJ will review and consult for submitters on the process of making files.
Some submitters use Nucleotide Sequence Submission System to submit a lot of sequences, while some submitter use MSS to submit a few sequences.
Based on above information, select either of them as needed.

Last Updated:July 3, 2014
How many data can I submit by using Mass Submission System? MSS submission

There is no limit of the number of entries to use Mass Submission System.
You can use it not only for many sequences but also for one long sequence with many features (i.e. complete genome with annotation).
See Mass Submission System

Last Updated:July 3, 2014
How can I check my sequence to exclude vector contamination? MSS NSSS submission
Last Updated:July 3, 2014
Is there any restriction of sequence length to submit to DDBJ? MSS NSSS submission
Upper limit
If the sequence is really observed, there is no upper limitation of the sequence length to submit to DDBJ.
However, we can not accept any operationally joined sequence, for example, joining chromosomes. We accept each chromosome sequence, respectively.
For sequences greater than 500 kbases in its length, please submit by using Mass Submission System (MSS) instead of Nucleotide Sequence Submission System (NSSS).
Lower limit
For minimum length, DDBJ has no systematic restriction, however, when the sequence is less than 20 bp in its length, our system outputs "warning" to your data.
When the sequence has biological significance, even if it is a short sequence, DDBJ accepts the submission of it. However, we consider that more than fifteen bases would be required to describe something in general, such as full length of small RNA transcript, some of specific tag sequence and so on.
Is there any case to reject submission to DDBJ?
Acceptable data for DDBJ
Last Updated:February 26, 2016
Sequence format acceptable for the submission (FASTA, multi-FASTA) MSS NSSS submission

For DDBJ nucleotide sequence submission system (NSSS), you must input nucleotide sequence(s) in FASTA format (for 1 sequence only) or in multi-FASTA format (for 2 or more sequences).
Related page: Format of the nucleotide sequences that you can paste or upload

You must insert the end flag (//) at the end of each sequence when you use MSS for the submission. Please see the page, "How to Make Sequence File".

See also Wikipedia, FASTA format

Last Updated:November 27, 2017
MSS application form is not displayed MSS submission
Depending on the country or area, MSS application form may not be displayed. If MSS application form is not displayed, please send the following items by e-mail.
Subject: MSS application
To: ad_mass
Body: (* Required)
About using MSS
・Have you ever used this system for your submission? * Yes / No
Contact Person Information
・Contact person's name *
・Contact person's E-mail address *
・Contact person's affiliation *
If you are not a contact person but a person in charge of the submission, please fill in the following items.
・E-mail address
Outline of your data
・When would you like to release the data? * Immediately / Hold until specified date (YYYY/MM/DD)
・Number of sequences *
・Sequencing Technology * (Please select one or more.) Sanger (gel/capillary) / Roche 454 / Illumina Solexa AB SOLiD / Other
・Data type * (Please select one or more.) EST / full length cDNA (HTC) / TSA*1 / GSS complete genome*2 / draft genome*2 (WGS or HTG) / Ohter
・Biological background * e.g.) 16S rRNA gene sequences from Bacillus bacteria. 1000 bp-1500 bp
・Supplementary Information
What is data type ?
In case of either *1 or *2, please take following steps before MSS submission.
Please register your project information in BioProject Database to get BioProject ID.
Please register biological source materials used in experimental assays in BioSample Database to get BioSample ID.
In case of *2, please also do the following procedure.
complete genome or draft genome with feature annotation, you also have to get a locus tag prefix through BioProject submission.
However, even though complete genomes, if the genome sequences are relatively small like as viruses, phages, organelles or plasmids only (i.e without chromosomes), you do not need to get BioProject ID.
Last Updated:August 25, 2017