Last updated:2014.7.7.

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

FAQs 35 : Tag = nsss-submission
Can we update submitted data with DDBJ Nucleotide Sequence Submission System? NSSS update

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.

Last Updated:June 9, 2014
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  • "Unpublished"; In cases of preparing paper, during paper submission, or you do not prepare any publication.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, see When our paper was published, what should I do? on Data Updates/Corrections and contact us from this form to send request with subject "Our paper was published".

Last Updated:June 19, 2014
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
Is FAX number required to submit sequence data? MSS NSSS submission

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.

Last Updated:June 19, 2014
How to describe a base substitution that causes an amino acid substitution? format NSSS 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.

Last Updated:June 26, 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
join(199001..199035,1..100)
See also Description of Location in detail.

Last Updated:June 30, 2014
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 confirmation screen.
Last Updated:June 30, 2014
I have not yet received accession number, how many days does it take to get accession number? NSSS submission

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".
Last Updated:July 3, 2014
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.

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.
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 can I check my sequence to exclude vector contamination? MSS NSSS submission
Last Updated:July 3, 2014
[Nucleotide Sequence Submission System] How to suspend and resume my submission? NSSS submission
Last Updated:July 3, 2014
[Nucleotide Sequence Submission System] How to entetr two or more features for a sequence? NSSS 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.

Last Updated:July 4, 2014
[Nucleotide Sequence Submission System] How can I describe DEFINITION? NSSS submission

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

Last Updated:July 4, 2014
[Nucleotide Sequence Submission System] Can not find input field for some qualifier NSSS submission

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)
Last Updated:July 4, 2014
[Nucleotide Sequence Submission System] How to fix error message: "First codon [***] is not a start codon." / "Final codon [***] is not a stop codon."? NSSS submission

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.

For example: partial CDS feature in the range, 1..295
location condition
<1..295 [not start with initiation codon] and [stop with termination codon]
1.. >295 [start with initiation codon] and [not stop with termination codon]
<1.. >295 [not start with initiation codon] and [not stop with termination codon]
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
Last Updated:July 7, 2014
[Nucleotide Sequence Submission System] How to fix error message: "To use [translation] qualifier, [exception] qualifier is required in the [CDS] feature." ? NSSS submission

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.
Last Updated:July 7, 2014
[Nucleotide Sequence Submission System] How to fix error message: "Invalid value [***] for [transl_table] qualifier."? NSSS submission

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
Last Updated:July 7, 2014
[Nucleotide Sequence Submission System] browser still waiting for response on the process of data input NSSS submission

At first, please save the URL of the page on Nucleotide Sequence Submission System.
Then, shutdown the browser and reopen the saved URL.
When your sequences are relatively many, 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
Last Updated:July 6, 2014
[Nucleotide Sequence Submission System] How to fix error message: "Value of [ codon_start ] is not 1, but [###..###] is 5' complete type."? NSSS submission

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."?
Last Updated:July 7, 2014
[Nucleotide Sequence Submission System] Can I modify descriptions on a previous page? NSSS submission

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.
Last Updated:July 7, 2014
[Nucleotide Sequence Submission System] I can not upload my annotation file NSSS submission

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".

Last Updated:July 7, 2014
[Nucleotide Sequence Submission System] How to submit more than one sequence at once? NSSS 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.
Last Updated:July 7, 2014
[Nucleotide Sequence Submission System] How to fix error message: "Stop codon ‘*’ is found in the range."? NSSS submission

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.

Last Updated:July 7, 2014
[Nucleotide Sequence Submission System] How to confirm translated amino acid sequences (i.e. /translation qualifier) for CDS features? NSSS submission

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.

References
How can I input amino acid sequnce (/translation qualifier) for CDS feature?
The amino acid sequence in the value of /translation qualifier seems to be incorrect.
Last Updated:July 7, 2014
[Nucleotide Sequence Submission System] How to fix error message: "MGA:No entry name is found other than [ COMMON ], without feature [ DATATYPE/type=MGA ]."? NSSS submission

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.

Last Updated:July 7, 2014
What are the browser that the DDBJ service supports? ARSA BLAST NSSS PR search
DDBJ recommend using the following OS and browsers to use our servises.
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
However, the OS, browser environment recommended above is subject to change without prior notice.
Last Updated:November 24, 2016
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.
References
Is there any case to reject submission to DDBJ?
Acceptable data for DDBJ
Last Updated:February 26, 2016
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