FAQ

Since DDBJ Nucleotide Sequence Submission System can be only used for new submissions, you can not update submitted data with the system.
For update, see Data Updates/Corrections.

Select from following two ways.

• DDBJ Nucleotide Sequence Submission System: an interactive application to enter all of items via web form
• Mass Submission System (MSS): to send submission files to DDBJ, directly

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.

See Organism qualifier.
For detail, see either of following cases;
2. In case of unidentified species names, proposing a new species etc.
3. environmental sample

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.

For description of organism qualifier, see 4. Artificially constructed sequences.

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

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• "Unpublished"; In cases of preparing paper, during paper submission, or you do not prepare any publication.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.

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• status: [Unpublished]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".

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.

In general, you can describe base substitutions by using variation feature with replace and note qualifiers.
In case of using DDBJ Nucleotide Sequence Submission System, select 'other' for template.
About format of feature annotation, see F01) polymorphism and variation at Example of 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
join(199001..199035,1..100)
See also Description of Location in detail.

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 confirmation screen.

In principle, accession numbers will be acknowledged to contact person via e-mail (with Subject: "[DDBJ] Assigned Accession No.") within 5 working days (i.e. except holidays) after DDBJ accepting submitted data.
See DDBJ Calendar about working days of DDBJ Center.
When you do not receive accession numbers or inquiry about your data from DDBJ within 5 working days after your data submission, please contact us from contact form by selecting the item, "Data Submission".

To make sure, Do not block E-mails from DDBJ.

In case of using DDBJ Nucleotide Sequence Submission System, please confirm if you have received a mail from DDBJ with "DDBJ: Web submission completed" in its subject or not. This mail is automatically sent to contact person, when DDBJ accepts your sequence data via Nucleotide Sequence Submission System.

If you have NOT received the mail,

Your submission is not yet finished, so, please complete your submission.

If you have received the mail,

please contact us from contact form with contact person E-mail address and EntryID of your data by selecting the item, "Data 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.

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.

References

[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.

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.

See Before your nucleotide sequence submission.
You can use VecScreen.

See How to suspend/resume the submission.

At 6. template, a) select 'other' and click [Input annotation] or b) Click [Upload annotation file].
Then, you can describe two or more features for each sequence as follows.
In case of a), see 7.Annotation (when “other” was selected at template).
In case of b), see 7. Annotation: upload an annotation file.

Since DEFINITION is constructed by DDBJ according to rules, there is no field to enter it.

Click [Select Qualifier], check qualifiers in the dialog as needed and click [Save] button.
Then, you can find input fields for qualifiers on 7.Annotation.

Related to this issue, in case of selecting "other" on 6. template, you have to specify some features other than source. So, click [Add feature] and select some feature on the list.

Reference

7.Annotation (when “other” was selected at template)

These errors mean amino acid translation for CDS (protein coding sequence) feature is not appropriate in the 5' or 3' end, respectively.
When the CDS feature is not complete (i.e. partial) at 5' and/or 3' ends, its location is required to include flag for 'not complete'.
According to rules on Description of Location, partial sequences should be appropriately specified with flags for 5' end not complete, "<", and/or for 3' end not complete, ">" on its feature location.

References

[Nucleotide Sequence Submission System] How to fix error message: “Stop codon ‘*’ is found in the range.”?

[Nucleotide Sequence Submission System] How to fix error message: "Value of [ codon_start ] is not 1, but [###..###] is 5' complete type."?

Offset of the frame at translation initiation by codon_start

This error message is outputted, because you select /translation for CDS feature by dialog of [Select Qualifier] button.
Generally, since /translation qualifier is automatically created according to items under CDS feature, do not enter any amino acid sequence.
So, you can fix the error by removing /translation qualifier.

For your information, /translation qualifier is required only in case describing with /exception qualifier.
Typically, /exception qualifier indicates "RNA editing" is occurred on mRNA. In that case, conceptual amino acid translation of genome sequence is different from protein product of real mRNA molecules.

References

Example of Submission: B09) RNA editing

How can I input amino acid sequence (/translation qualifier) for CDS feature?

[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.

The error is occurred because you do not enter correct genetic code.
See 7.Annotation -- How to input an organism name.
To specify genetic code, enter digit in the input field.
The value will be automatically applied for /transl_table qualifier for CDS feature.

For your information, in case of a previously reported organism, the genetic code is automatically specified, by describing Scientific name (/organism qualifier) and /organelle qualifier. If your sequence is derived from an organelle other than nuclei, you have to specify /organelle qualifier to set the genetic code for mitochondrion, chloroplast or some, appropriately.

References

7.Annotation

7.Annotation – How to input an organism name

The Genetic Codes

About /transl_table qualifier

At first, please save the URL of the page of Nucleotide Sequence Submission System.
Then, clear cache of the browser and reopen the saved URL.
It is likely to resolve the condition.

If not resolved, confirm if you use either of browsers Firefox or Chrome that we recommend to use.
If not, change to Firefox or Chrome and reopen the URL.

If you still have any problem, please contact us with followings from contact form by selecting the item, "DDBJ Nucleotide Sequence Submission System".

• URL
• Number of your sequences
• OS: Windows, MacOSX, or Linux, and its version
• Browser: software and its version

You may enter incorrect values for Location and/or /codon_start of CDS feature.
If the value of /codon_start is either of "2" or "3", the location of CDS feature should be 5' end not complete.

See Description of Location and modify the location with flag for "5' end not complete", for an example, from "1..300" to "<1..300".
When the CDS feature is started with an initiation codon, correct /codon_start with "1".

References:

Offset of the frame at translation initiation by codon_start

[Nucleotide Sequence Submission System] How to fix error message: "First codon [***] is not a start codon." / "Final codon [***] is not a stop codon."?

[Nucleotide Sequence Submission System] How to fix error message: "Stop codon ‘*’ is found in the range."?

You can modify your inputs on any pages before finishing your submission.
You can go back to each page by clicking either of 1.Contact person, 2.Hold date, 3.Submitter, 4.Reference, 5.Sequence, 6.Template or 7.Annotation in progress bar at upside of pages.

※Caution

After inputting feature annotation on 7.Annotation, if you do either of followings, feature annotation will be removed.

• modify your sequences on 5.Sequence
• change your template on 6.Template

Confirm following points.

• You have to input the same entry names for both sequences and in annotation file.
• The format of annotation file must be tab delimited text consisting with 5 columns.
• The line feed code of annotation file must be in LF (unix format) or CR-LF (windows format).
• You have to use correct names for feature and qualifier keys.

If you still have any problem, contact us from contact form by selecting the item, "Data Submission".

On 5.Sequence, input all of your sequences in multi-FASTA format. We will assign consequent accession numbers for your sequences.
Moving to 7.Annotation, you can enter feature annotation for each sequence at once.

Caution

※ All of following items must be unified for all sequences. You can not specify thenm for each sequence.

• Contact person
• Hold date
• Submitter
• Reference

※ You can select only one template on 6.Template for all sequences. You can not select a template for each sequence.

In general, see How to describe CDS feature, when termination codon is found in the range.
You can also see Protein Coding Sequence; CDS feature to describe CDS feature.
Following items are case study for the error.

1. Did you correctly specify /codon_start qualifier to indicate reading frame of the CDS feature?
  Select 1, 2 or 3, appropriately.

References:

Offset of the frame at translation initiation by codon_start

[Nucleotide Sequence Submission System] How to fix error message: “First codon [***] is not a start codon.” / “Final codon [***] is not a stop codon.”?

[Nucleotide Sequence Submission System] How to fix error message: "Value of [ codon_start ] is not 1, but [###..###] is 5' complete type."?

2. Have you specify correct genetic code for /transl_table qualifier?
See followings and specify genetic code, appropriately.

References

The Genetic Codes

About /transl_table qualifier

[Nucleotide Sequence Submission System] How to fix error message: "Invalid value [***] for [transl_table] qualifier."?

3. Are there really some stop codons in the range of CDS feature because of frame shift, nonsense mutation, or some other reason?

3-1. In case of pseudogene
Click [Select Qualifier] button beside CDS and add /pseudogene qualifier. Then, you can specify /pseudogene qualifier with its controlled vocabularies.
See also b) considered pseudogene in detail.

3-2. In cases of unsure whether it is pseudogene or not, the reason of stop codon is uncertain, or on the process of diversity increasing related to acquired immunity, describe misc_feature, not CDS feature.
See a) Putative nonsense mutation, frameshift caused by uncertain reason, or on the process of diversity increasing related to acquired immunity for IgG etc. in detail.

In other cases. There are some possibilities to output this error because of ribosomal slippage, RNA editing, exceptional amino acid usage, transpon insertion and so on.

You can confirm amino acid sequences for CDS features as follows.

1. Download UME_win.zip (for Windows) or UME_mac.zip (for MacOSX) from Mass Submission System.

2. Download both annotation and sequence files at 8. Finish on DDBJ Nucleotide Sequence Submission System.

3. Run UME and load both annotation and sequence files. Then click [Execute] of transChecker.

The function to confirm amino acid sequences will be applied on DDBJ Nucleotide Sequence Submission System.

Though you have not yet enter either /organism or /mol_type on annotation table, you click [Confirm] button.
You must fill mandatory items of annotation (feature, location, qualifier) before clicking [Confirm] button.

On 7.Annotation, click [Select Qualifier] button beside 'source', and select qualifiers as needed. Then, click [Edit] button beside entry name and input /organism and others. Note that it is required to input at least one feature other than source.
See also 7.Annotation – How to input an organism name.

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

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.

References

Is there any case to reject submission to DDBJ?

Acceptable data for DDBJ

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