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.
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.
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.
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.
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".
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.
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
See also Description of Location in detail.
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.
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 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.
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.
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.
|<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]|
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.
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.
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 you still have any problem, please contact us with followings from contact form by selecting the item, "DDBJ Nucleotide Sequence Submission System".
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".
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.
Confirm following points.
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.
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.
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.
You can confirm amino acid sequences for CDS features as follows.
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.