Last updated:2014.7.7.

FAQ

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

FAQs 28 : Tag = format
How to submit only annotation for previously reported sequences? format submission

If your annotation meets the requirements of TPA Submission Guidelines, DDBJ can accept it as TPA (Third Party Data).

Last Updated:August 27, 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
How to submit sequence data related to Barcode of Life (BoL)? format submission

For sequence data related to Barcode of Life project, please submit via DDBJ Nucleotide Sequence Submission System or Mass Submission System.
For chromatograms (traces), please submit to DDBJ Trace Archive

Last Updated:June 18, 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
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
After submission of SNP data to DDBJ, will it automatically reflect to dbSNP? format submission

Though you can submit sequence data including SNP (Single Nucleotide Polymorphisms) to DDBJ, the data will not automatically reflect to dbSNP.
dbSNP is an independent database from INSDC, operated by NCBI.
For SNP data, we recommend you to submit to dbSNP.

In case of submission to DDBJ, see format of feature annotation at B13) polymorphism and variation on Example of Submission.

References
Where to submit variation data, such as single nucleotide variations, structural variations, copy number variations (CNVs) and so on?
How to submit sequence data related to DNA polymorphism?
Last Updated:February 26, 2016
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
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
When the correspondences between nucleotides and amino acids are different from the standard genetic code, how to describe CDS feature? format submission

At first, please confirm whether The Genetic Code is appropriately selected or not.
Generally, if /transl_table qualifier is appropriately described with a number of the genetic code, the nucleotide sequence is automatically translated to amino acid sequence according to the genetic code.

In exceptional cases of specific codons (selenocysteine etc.) that is not followed the genetic codes, describe /transl_except qualifier, appropriately.

In cases of RNA editing,ribosomal frameshiftmitochondrial TAA stop codon, see Example of submission and describe with /exception and /translation, /ribosomal_slippage, /transl_except, respectively.

In case of rare initiation of translation, staring with an amino acid other than methionine, describe the location of CDS feature with starting from "<", operatively indicating 5'end not complete. And describe brief explanation about the translation mechanism in /note qualifier.

Last Updated:June 30, 2014
Who should be the Contact person? format submission

See Contact person.
If your affiliation was changed after sequencing or when you belong two or more institutes, please describe the most responsible one as a representative.

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 page.
Last Updated:November 27, 2017
How to contact the submitter of sequence data? format search

Since 2007, we have removed E-mail addresses and phone numbers from sequence data.
If you can find a related paper at REFERENCE on DDBJ flat file, contact information would be available on the paper.
When you wishes to contact to the submitter(s) of an entry of your interest, please contact us via Inquiry to the sequence submitters (submitted to DDBJ) with reasons briefly, then we will forward your message to the submitter(s).

Last Updated:June 30, 2014
What is the date in LOCUS line? format search

It is the date of the last release of the data. See LOCUS of Explanation of DDBJ flat file format.

Last Updated:July 2, 2014
Is there any reference for Feature/Qualifier? format search submission
I would like to know the date when the data was submitted. format search submission

In general, you can find accept date in JOURNAL line of REFERENCE 1 on DDBJ flat file.
Please note that some old data do not have the description of accept date.

Last Updated:July 1, 2014
Can not find the sequence data, though the accession number cited on a paper. format search

DDBJ releases sequence data submitted with a hold date according to Principle of “Hold-Until-Published” data release.

Please confirm if the ID on the paper is Accession Number Assigned by INSD or not.

If accession numbers on the paper, please contact us from contact form by selecting the item, "Updating Submitted Data" with following items.

  • Accession numbers on the paper
  • Title of the paper
  • Authors
  • Journal name
  • Volume, pages, year
  • DOI, PubMed ID, URL
Last Updated:June 16, 2017
How are the data released from DDBJ published at EMBL-Bank, GenBank? format search

DDBJ is functioning as one of the international nucleotide sequence databases, including EMBL-Bank/EBI in Europe and GenBank/NCBI in the USA as the two other members.
When DDBJ releases the submitted data, EMBL-Bank and GenBank will load the data into their own services, respectively.
See Sequence Data Transition.
Note that the data are converted into EMBL-Bank or GenBank format.

Last Updated:June 8, 2015
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
The amino acid sequence in the value of /translation qualifier seems to be incorrect. format search submission

The rule to translate nucleotide sequence into amino acid sequence is specified in accordance with agreements of International Nucleotide Sequence Database Collaboration.
The codon table using a CDS feature is specified in the value of /transl_table qualifier as a number of The Genetic Codes.

There are three points frequently misunderstood.

  • You should specify /organelle qualifier to assign correct genetic code for mitochondrion or chloroplast.
  • The initiation codon is M, Met, methyonine, not G or V.
        See Start codon and N-Formylmethionine
  • When an amino acid can be specified by two bases (i.e. degeneracy of codons), it will be outputted.

There are some exceptional cases, represented by RNA editing and so on.

Last Updated:July 3, 2014
What is secondary accession number? format search submission update

INSD; International Nucleotide Sequence Database are composed of DDBJ, ENA and NCBI, and collect experimentally determined nucleotide sequence data.
A unique accession number issued by INSD for each submitted sequence data is defined as the INSD accession number.
On DDBJ flat file, the accession number is described in ACCESSION line.

If multiple entries are united to an entry, or if an entry is extensively modified after the submission, the responsible data banks may assign a new accession number to it. In these cases, the new accession number is called the primary accession number, and the old accession number(s) is/are called the secondary accession number(s).

In the flat file, the primary accession number is indicated first, then the secondary accession number(s) follows.

example
ACCESSION   AB999999 AB888888 AB777777
AB999999 -- primary accession number
AB888888 AB777777 -- secondary accession number

You can find the same updated entry with both the primary and the secondary accession numbers, in general.
However, if the old entry with secondary accession number has previously been open to the public, the old one is not removed. So, you can find the old record by getentry.

References
getentry HELP
INSDC Status Document: Replaced
Why is the retracted data still available?
Last Updated:July 7, 2014
We would like to acknowledge the NIG Supercomputer System in our publication. analysis format search

The activity of the NIG Supercomputer System are evaluated by the acknowledgments of all of you.
Please acknowledge in your papers, presentations and other publications, the role of NIG Supercomputer System played in your research.
It is no problem to modify the following example for the connection of sentences.


Computations were partially performed on the NIG supercomputer at ROIS National Institute of Genetics.


Last Updated:June 26, 2017
We would like to acknowledge DDBJ in our publication. analysis format search

When you use DDBJ services in your research, we would appreciate it if you would include a reference to DDBJ in your publications.
If you consider citation of DDBJ paper is unsuitable, please consider to acknowledge in your publications, the role of DDBJ services played in your research.
It is no problem to modify the following example for the connection of sentences.


This research was performed using "name of DDBJ Service, analytical tools".


Last Updated:June 26, 2017
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