When there are many Experiment and Run objects, create metadata XMLs by
using the excel for the DRA metadata and the XML generator. The metadata
can be registered by uploading the Submission/Experiment/Run XMLs in
D-way. Please see the GitHub
page for details.
Divide sequence data files per sample and submit each file as single BioSample-Experiment-Run set. If you need to describe the relationship between barcode sequence and sample, please describe in the Library Construction Protocol of Experiment as free-text.
data excessive while validating formatter within short read archive module - cumulative length of reads data in file(s): 152 is greater than spot length declared in experiment: 76 in spot ‘xxxx’
Spot length value in Experiment differs from actual read length. For paired library, enter a sum of paired read lengths in the Spot length.
fastq-load err: data inconsistent while validating formatter within short read archive module - cumulative length of reads data in file(s): 70 is less than spot length declared in experiment: 152, most probably mate-pair is absent in spot ‘xxxx’
When ‘fastq’ is selected for the filetype in Run, “read length should be constant” and “paired reads must appear in the same order in the paired files”. If the fastq files do not meet these conditions, validation errors occur. Revise the filetype from ‘fastq’ to ‘generic_fastq’.
constraint violated while executing function within virtual database module
-M 25: Minimum read length to output is 25 (default is 25)
-E: No sequences starting or ending with >= 10N
--skip-technical: Dump only biological reads
--split-3: Legacy 3-file splitting for mate-pairs: first and second biological reads satisfying dumping conditions are placed in files *_1.fastq and *_2.fastq, respectively. If only one biological read is present, it is placed in *.fastq.
-W: Apply left and right clips
Reads are filtered and trimmed according to above dumping conditions, reads number of fastq is generally less than that of SRA file.Users can generate unfiltered and untrimmed fastq files by using following fastq-dump options.
Aspera ascp command line client can be dowloaded
here.Please select
the correct operating system. The ascp command line client is
distributed as part of the Aspera connect high-performance transfer
browser plug-in.
Your command should look similar to this:
ascp -i <aspera connect SSH key> <option> -P 33001 anonftp@ascp.ddbj.nig.ac.jp:<file or files to download> <download location>
When sequencing data derived from relevant samples are deposited in DDBJ Sequence Database and DRA, please add publication information as described above.
For a publication about isolation and growth condition specifications of the organism/material, add pubmed id etc to isol_growth_condt.
For a primary genome report, please add the relevant pubmed id etc to ref_biomaterial.
Please login to the submission system
and change the date.
You can set the hold date for a maximum of 4 years,
and this date may be brought forward or pushed back at any time.
We will send you an e-mail reminder 30 days before the scheduled release
date, inviting you to postpone the release date as necessary.
Please see the video tutorial.
BioProject and BioSample submissions must be made through the Submission Portal D-way. Once you begin a BioProject or BioSample submission, it will be assigned a temporary tracking ID (PSUB/SSUB[number], respectively) – this is not the final accession!
Once a BioProject is complete, it is assigned an accession like PRJDB[number]. Once a BioSample submission is complete, each sample will receive an accession like SAMD[number].
When creating DRA experiments, please specify the PSUB ID or PRJDB[number] accession as your BioProject, and SSUB ID or SAMD[number] as your BioSample. Note that a given data file can be linked to a single BioSample only.
When sample preparation and sequencing are carried out by different research groups, submitting DRA Experiment can refer BioProject and BioSample IDs obtained in the other submission account. If you need to refer external BioProject and BioSample IDs, contact to the DRA team. When referencing external objects, please be aware of triggering of data release among BioProject, BioSample and DRA submissions.
BioSample is descriptive information about the biological source
materials, or samples, used to generate experimental data in any of
primary data archives. Biological and technical replicates need to be
registered as separate BioSamples distinguished by the “replicate”
attribute having values such as “biological replicate 1” and “biological
replicate 2”.
Each SRA Experiment is a unique sequencing library for a specific
sample. Importantly, much of the descriptive information that is
displayed in the public record of your data is captured at the level of
the DRA Experiment.
SRA Runs are simply a manifest of data file(s) that should be linked to
a given sequencing library – no information present in the Run is
displayed on the public record of your project. Note that all data files
listed in a Run will be merged into a single SRA archive file (and fastq
file for distribution), so files from different samples should not be
grouped in the same Run. Paired-end data files (forward/reverse),
conversely, MUST be listed in a single run in order for the two files to
be correctly processed as paired-end. Do not divide a sample for a
paired-end library (for example, forward and reverse).
MD5 checksums are used by the DRA to verify the integrity of transmitted data. MD5 checksums are a 32-character alphanumeric string like. Please refer to the manual.
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.
In principle, DDBJ only accepts updating requests from the original submitter of the entry except reference update. Therefore, if you are not the submitter you will need authorization from the submitter before making requests for the entry. DDBJ can forward your comments and suggestions to the submitter. Please contact us via Inquiry to the sequence submitters (submitted to DDBJ).
We only accept this kind of request from the original
submitter of the entry.
Please contact us from contact form by
selecting the item, “Updating Submitted Data” with accession numbers.
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.
If you are making update request for large number of entries, or many changes of features/locations/qualifiers due to sequence modification, see followings.
(1) Update information is in common of all entries.
Example: change reference or submitters information, postpone the hold-date, etc..
(2) Contents of corrections are different among entries.
Example: change each clone or gene name of all entries, etc..
(3) Extensive correction of data
Example: change more than 30 features due to the sequence update, etc..
In case of (2) or (3), we would like to know the number of entries, the correction item, etc. to specify the file format for your request. Contact us in advance from contact form. In general, we handle update requests within several days but for a large number of entries, it might take us time in updating the data. Be sure to contact us beforehand when you request the release of data which accompanies correction.
DDBJ does not provide any procedure for a limited disclosure by the password authentication or else. When you have to show your sequence data submitted with "Hold-Until-Published" status for only particular individuals, you can send as a text file including your sequences to them. If the referee wish to confirm the condition and/or the descriptions of your sequence submission, you can choose either of the following two procedures;
a) Publish your sequences through DDBJ.
If you do not mind to open your sequences to the public, please send us your request to publicize your submitted sequences with all of accession numbers.
b) Send DDBJ flat files of your submission to the referee, directly
When the submitter requests to us, we send the text file including DDBJ flat files to the submitter. So, please send us your request with all of accession numbers to get DDBJ flat file(s) of your submission. Then, you can forward the text file to the referee.
For once published entries, we can restrict to use the data, if the conditions are right. In case of the restriction, DDBJ will not include the data in its periodical release and remove from all services under DDBJ. However, the data is permanently available on getentry queried with its accession number. # The rule is not applied, when the data is published by any mistake of INSD. This policy is written in the document prepared by International Advisory Committee of INSD on Overview of International Nucleotide Sequence Databases Policies as follows;
All database records submitted to the INSD will remain an entry accessible as part of the scientific record. Corrections of errors and update of the records by authors are welcome and erroneous records may be removed from the next database release, but all will remain permanently accessible by accession number.
In addition, there are a number of databases constructed by occasionally using data from INSD. DDBJ can not support to delete data from such databases. If you are to delete the cited data on other databases, you have to contact managing staff of each database, directly.
DDBJ does not accept any reservation for updating sequence data.
Therefore, in case of updating published data, the data will be
immediately re-distributed after update.
Please select either of following ways.
In this time, canceling the request for update, when you can publish
updated data, contact us again.
Submit the updated data as a new data with hold
date. When the new data is
published, the accession number of the old data will become a
secondary accession number for the new data.
# Please inform us during submitting the new data to link it to the
old data.
In principle, DDBJ can not restore any published data. See also following item about access restriction.
In principle, you cannot remove your sequence data from DDBJ retrieval system: getentry, if it has already been open to the public (If DDBJ wrongly published your data because of any mistakes, the data should be removed as soon as possible.).
However, if there is some specific reason for removing your sequence data (i.e. some error is found, etc.), we can restrict access to your sequence data.
Please send your request from contact form with the following contents.
Accession numbers:
Reason in brief:
New hold-date: (e.g. 2019/06/25)
If we restrict access to your sequence data and remove it from the public view, then it will no longer be included in homology search services at DDBJ or distributed as a part of the next DDBJ periodical release. However, it may remain in other third party databases, and will still be retrievable in getentry by accession number based queries.
Moreover, our unified database may be copied and redistributed without permission at any other organizations. In case you need to withdraw your entry from such database, we ask you to make request directly to the organization which manages the database.
In principle, following two conditions are required to delete your
sequence data;
The sequence data has not yet been publicized
The accession number of the data has not yet been
published.
Please send your request from contact
form with the following contents in clear
English.
Accession numbers:
Reason in brief:
Just for information, we can restrict access to your sequence data that
have been open to the public, if the conditions are
right.
See also the following item.
It is getentry. "getentry" is a system for data retrieval by accession numbers, etc. In general, the sequence data will be available on getentry from the day after processed to release.
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.
In general, you can submit amino acid sequences by describing CDS feature for your nucleotide sequences. However, DDBJ does not accept amino acid sequences only, i.e. without any nucleotide sequences. In that case, please submit to UniProt, directly. You can submit amino acid sequences to UniProt through SPIN. Please contact to datasubs@ebi.ac.uk.
DDBJ can not accept only assembled EST sequences. However, DDBJ can accept EST assembled sequences as TSA with original (i.e. before assemble) sequence data. See also Data Submission form Transcriptome Project. When original sequence data (primary entries) are generated from Next Generation Sequencers, submit to DDBJ sequence Read Archive (DRA), from traditional sequencers, submit as EST via Mass Submission System (MSS). Then, DDBJ can accept assembled sequences (both de novo and reference mapping) as TSA through MSS.
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.
Generally, DDBJ do not need any offprint to process your data. Occasionally, DDBJ may contact the submitter of sequence data to ask sending an offprint, if necessary.
When you kindly describe about using DDBJ on academic papers etc., in
general, please use the latest article for
DDBJ on Nucleic Acids Res. Database issue
as a reference.
However, please note followings.
In case of citation for each sequence record
In general, it is enough to describe accession number for it in your publication.
If you discuss about the data in detail, please use primary
citation for the data as a reference.
In case of citation for each service provided at DDBJ
Basically, please submit every sequence that you have experimentally determined, whatever the resource of genome, mRNA or any others. In principle, DDBJ accepts submission of experimentally determined sequence in its contiguous structure. You can describe mRNA feature, CDS feature and so on as annotation for genomic sequence, however, descriptions of mRNA features do not mean "the mRNA sequence is experimentally determined.", in general. If you have read mRNA sequences, please submit mRNA sequences to DDBJ. See also Acceptable data for DDBJ.
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.
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".
Though there is no requirement to submit sequence data to DDBJ (, EMBL-Bank or GenBank) on the journal, we strongly recommend to submit sequence data to DDBJ for improvement of data availability for readers of your paper.
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.
When sequence data are published, the data will be shared among DDBJ, EMBL-Bank and GenBank. So, it is necessary and sufficient to submit sequence data to either of three data banks only once. If you submit sequence data to GenBank after submission of the same data to DDBJ, the data will be duplicated. So, do not submit the same data to two or more data banks.
Though some journals instruct to authors to submit sequence data to GenBank, Accession Number is commonly used by all of DDBJ, EMBL-Bank and GenBank to construct INSD.
Nucleotide sequence data related to patent applications are transferred from Japan Patent Office to DDBJ. So, usually, you do not have to submit such sequence data to DDBJ.
However, if you apply to any other Patent Office, or if you need to publish a paper during patent application, confirm at Patent Office whether you can submit the data to DDBJ or not.
Note that when the sequence data is published from DDBJ, the data becomes a part of the public domain, as "official notice".
If you submit nucleotide sequence data to DDBJ, you can get
NO priority for the data. DDBJ takes no responsibility for any property or priority issues for patenting. For patent application, you should confirm JPO or some other Patent Offices.
DDBJ does not have any right for the gene nomenclature. Also, DDBJ does
not make any official collaboration with any committee of gene
nomenclature. If there is no particular incident, the descriptions
related to gene nomenclature are described as provided by submitter.
Even if you name a gene during your sequence data submission to DDBJ,
there is no guarantee that the gene name is accepted at research
communities.
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.
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.
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.
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 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.
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.
We cannot answer the days to issue accession number(s) because it depend on the contents of your submission.
If you do not receive any email from DDBJ after 5 working days, please contact us from contact form.
In case of using DDBJ Nucleotide Sequence Submission System, please confirm whether 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 Submission ID of your data.
If you have specific ID for your data other than accession number, such as EntryID or any, contact us from contact form with ID and E-mail address of contact person. In case of uncertain, tell us following items as far as you know, then we will search your data.
Your name
Your affiliation at the time of submission
Your current affiliation
Your mail address at the time of submission
Your current mail address
The date, month and/or year, when you submit your data
Tool that you used to submit your sequence
Your sequence(s) (if many, just a few representatives)
Biological feature of your sequence
When we can not find your data, we will ask you to submit your data as new one.
In general, see the rule of the journal (i.e. Instructions to Authors), and follow it.
At INSDC, we recommend you to describe accession numbers in the footnote on the title page of your paper as following;
Note: Nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession number(s)—-‘.
It indicates that this data is directly submitted from the submitter. The term is the antonym to "journal scan". REFERENCE 1 is the information of submitter(s), not general reference. So, do not describe "Direct Submission" in the title for literature in REFERENCE 2 or after.
If the information of contact person is old or invalid, we may be unable to acknowledge publication of your data or any other important announcement.
Contact us from this form to send request by selecting the subject, “Change the contact person, belonging, institution, etc..”.
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.
In case of the meantime of data distribution:
The data may be on the process of data distribution. If you are
unable to retrieve the data longer than a week, please send us an
inquiry including the accession number from contact
form.
In case of not yet confirmed the accession number is published
on a paper or others:
Please let us know the paper or other media in which the accession
number is described.
In case of the data submitted BEFORE January 1, 1998:
The sequence data be still unpublished after hold
date.
In case of 3 or 4, we will check and support it.
Please contact us from contact form by
selecting the item, “Updating Submitted Data” with accession numbers.
See "Why is the hold-date required?". Please specify the date. Though DDBJ does not restrict the date, we strongly recommend to specify the date within two years. If not specified, the data will be published, immediately.
After data submission, you can change the hold date as needed. Contact us from this form by selecting "Change the hold-date" in [Subject].
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.
In general, the data released from EMBL-Bank or GenBank are loaded into DDBJ services and published from DDBJ within their released date. The data released from DDBJ are loaded into ENA/EBI and GenBank and published from them within a few days. However, the data release processes at all three databases may be delayed, because of system maintenance, troubles on the network, or any other reasons. So, we can not specify the temporal differences among them.
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.
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
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.
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.
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]
For example: partial CDS feature in the range, 1..295
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.
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 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”.
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”.
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.
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.
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 – Organism
name.
In the Environment Ontology (ENVO), the biome [ENVO_00000428] classes are subclasses of environmental system.The env_biome represents
environmental systems to which resident ecological communities have
evolved adaptations.Thus, a env_biome may be thought of as a
community-centric ecosystem, whose extent is defined by the presence of
the communities adapted to it.This requires that a env_biome possesses
a degree of spatial and temporal stability that has allowed at least
some of its constituent communities to adapt.Classes such as tundra
biome
[ENVO_01000180]
and coniferous forest biome
[ENVO_01000196]
are included in ENVO.Currently, the biome branch of the ontology makes
no commitment to a specific spatial or temporal scale.
The biome described above are useful in ecological settings; however,
environments are often described by referencing a single entity that has
a strong causal influence on its surrounding space.For example, a coral
reef environment is determined by the presence and influence of a coral
reef
[ENVO_00000150].Similarly,
the human gut environment is determined by the human gut.Removal of
either the coral reef or the human gut would cause the associated
environmental system to collapse.Environmental systems of this kind make
no specific reference to ecological communities or populations (as do
biomes),but to some central, supporting ‘feature’.Entities that act in
this way as the causal ‘hubs’ or supports of a given environmental
system are referenced by classes in ENVO’s top-level environmental
feature
[ENVO_00002297]
hierarchy.For example, the environmental feature seamount
[ENVO_00000264]
would support a seamount environment, i.e. an environmental system which
is supported by, and whose properties are determined by, the presence of
a seamount.
In contrast to the classes above, which identify countable entities, the
subclasses of the top-level environmental material
[ENVO_00010483]
class refer to masses, volumes, or other portions of some medium
included in an environmental system. A portion of environmental material
is understood to be more complex and variable in composition than a
simple collection of material entities (e.g. a collection of silicate
particles). For example, the environmental material soil
[ENVO_00001998]
typically contains aggregates of fine rock particles, sand grains, clay
particles, silt particles, communities of animals, plants, fungi and
microbes, small parts of organisms, organic matter, water inclusions,
and airspaces.
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 AB999999AB888888AB777777
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.
Authentification is by using SSH key not by password.
A private key is pair of a public key registered in a D-way submission account.
A private key file has read permission.
A private key file permission is set as others cannot access. For example, rw-------.
A passphrase for private key is correctly entered.
When transferring data files by using a private key generated in the other operating system, please check format of a private key. Convert private key
In Unix/Mac OS X: Convert a key in the Windows PuTTY file format into the OpenSSH.
In Windows WinSCP: Convert a key in the Unix/Mac OS X OpenSSH file format into the Windows PuTTY format.
When these are correct, because we do not support technical details regarding use of third-party softwares, please refer to websites of softwares or confirm your system administrators whether scp (port 22) is allowed or not.
To merge genome sequencing and transcriptome analysis projects, select both 'Genome Sequencing' and 'Transcriptome or Gene Expression' for the Project data type. One material is allowed for the Material, so select 'Other'.
Another way is to register 'Genome Sequencing' and 'Transcriptome or Gene Expression' as separate projects and unite them by an Umbrella BioProject.
Linked [BioProject](/bioproject/index-e.html),
[BioSample](/biosample/index-e.html), [DDBJ](/ddbj/submission.html) and
[DRA](/dra/index-e.html) data are released as follows.
- Release of the BioProject and BioSample records DO NOT trigger release of the
other linked data.
- Release of the BioSample records trigger release of the referencing
BioSample in derived_from attributes.
- Release of the DDBJ and DRA nucleotide sequence data DO trigger
release of the linked BioProject and BioSample records.
- Release of the DRA data DO NOT trigger release of the DDBJ records.
All metadata and sequencing data in a DRA submission are released at
once.
Release of linked BioProject/BioSample/sequence records
DRA Handbook: [Release of DRA](/dra/submission.html#data-release)
BioProject Handbook: [Release of
BioProject](/bioproject/submission.html#data-release)
BioSample Handbook: [Release of
BioSample](/biosample/submission.html#sample-release)
Uploaded data files are processed per Run. All files under a Run are
merged into single [binary SRA
file](http://www.ncbi.nlm.nih.gov/books/NBK47539/#SRA_Overview_BK.SRA_Architecture)
by using [SRA
toolkit](http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc).
During this conversion, length and format of all reads are checked.
Read names are editted and identifiers (DRR accession number + serial
number) are automatically inserted ([example:
DRR000001](http://trace.ncbi.nlm.nih.gov/Traces/sra/?view=run_browser&run=DRR000001)).
Original read names should be unique in a Run.
A DRR accession number is used as a filename. If the
["generic\_fastq"](/dra/submission-e.html#File_Type) is selected for the
filetype, read names are replaced with the DRR accession number + serial
number. ([example:
DRR030615](http://trace.ncbi.nlm.nih.gov/Traces/sra/?view=run_browser&run=DRR030615)).
Example of read names:
``` code
@DRR000001.1 3060N:7:1:1116:340 length=36nnGATGGTAAGATAGAAGCAGTTGAAGTTTACAAACCGnn+DRR000001.1 3060N:7:1:1116:340 length=36nnIIIII%IIIIIIIIII7IHII26:C6EI)+,9,%%*nn@DRR000001.2 3060N:7:1:1114:186 length=36nnGATATTGGCCTGCAGAAGTTCTTCCTGAAAGATGATnn+DRR000001.2 3060N:7:1:1114:186 length=36nnIIIIIIIIIIIIIGI8IIDI6II;?:,+9+>.A1,Inn@DRR000001.3 3060N:7:1:945:361 length=36nnGTCAGGATCGGTCTCGCCTTTTAATAGAGGGAGATAnn+DRR000001.3 3060N:7:1:945:361 length=36nnIIIIIIIIIIIIIIII=3IIII>>I;-52/./+.I,
```
When "PAIRED" is selected in Experiment, paired reads are grouped in a
Run.
DRA generates fastq from SRA files by using [SRA
toolkit](http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc)
and provide sequencing data in both file formats.
More than two fastq files are provided for paired reads. Paired reads
are divided into a file with "\_1" (example, DRR000001\_1.fastq.bz2) and
"\_2" (example, DRR000001\_2.fastq.bz2). Reads without pair are provided
in a file without "\_1" nor "\_2" (example, DRR000001.fastq.bz2).
If multiple cultured genomes are part of the same research effort, then
they can belong to the same BioProject. However, each culture must be
registered as a separate BioSample.
Metagenomic assemblies, where multiple genomes are assembled with high
confidence from a single metagenomic sample, register a BioProject for
metagenomic assembly project, and BioSamples for each sample of
metagenomic assembly.
The E value is computed using the following formula, in which l denotes
the length of the query string, n denotes the number of strings stored
in the database, and S is a score that measures the homology between
nucleic acids or between amino acids. Note that k and m are positive
constants.
E=k\*l\*n\*exp^(－mS)
If the BLAST output results computed using this formula are displayed in
the form 1E-X, this means that the quantity has the value
10-X.
BLAST search results are displayed in descending order of homology score. There is no way to assign priorities to strings with identical scores, so there is no particular regularity to the order in which such strings are displayed.
If the number of search results shown is fewer than the number specified for the options “Number of Search Results to Display” and “Number of Alignments to Display,” you may increase the number of displayed results by increasing the value of the “Expectation value” under the “Advanced settings” field. In such a case, try setting the expectation value to an extremely large number such as 10,000. Note that, if the string is too short (a sequence length of 10 or so), BLAST will frequently be unable to find matches.
The sequence that you
entered was filtered by the BLAST program.
The filtering has the effect
of replacing regions of your input sequence of low structural complexity
with “N” (or “X” for amino-acid sequences). For details on filtering,
see the section “[FILTER](/services/blast-e.html#filter)” in the BLAST HELP. To
disable filtering, select the OFF radio button in the “FILTER” option in
the lower portion of the Settings screen.
Note with caution that setting
this option to “OFF” may result in search times that are longer than
normal.
Search results are displayed in the following order.
Precedence table of sequences with high homology scores
Homologous sequences and their alignment
Parameters and statistics
Note that the symbol “|” in the BLAST search results for nucleotide sequences indicates agreement between nucleotide sequences. For amino-acid sequences, matching amino acids will be displayed. The symbol “+” is used to indicate similarities between amino acids.
For further details, refer the original papers on BLAST.
The format differs from journal to
journal; please ask the publisher.
In your publications, please cite the
original papers for the appropriate tools and state that you used DDBJ
software for searching and analyzing gene sequence data.
Please see the DDBJ home page [References](/services/references-e.html)
about the original papers and other related papers on the DDBJ search
and analysis software.
The DDBJ/EMBL/GenBank data banks share
the sequences stored within each data bank, and in principle all three
data banks should contain the same data. However, due to time delays in
the inter-data-bank sharing of data released by individual data banks,
as well as delays between the time at which data are entered into a data
bank and the time at which the data are reflected in the corresponding
search service, searches conducted using different services at the
similar time on the same day may yield slightly different results. If
you do not obtain the search results that you were expecting, time
delays of this sort are the most likely culprit; however, for cases
requiring a more detailed investigation, please contact the DDBJ via the
“Other general questions” section of the contact portal. In this case,
make sure to specify the following information:
- The name of the search program and/or the URL that you used to
conduct the search.
- The search conditions that you used.
- The date and time at which you conducted the search.
- Accession number of the entry that should have been found.
- URL of the search results.
- Any other relevant information.
Also, please see the sections of this document corresponding to the
following questions.
- [Can not find the sequence data, though the accession number cited
on a
paper.](/faq/en/cannot-find-accession-number-cited-paper-e.html)
- [I am having trouble finding an accession number that should be
publicly available.](/faq/en/cannot-find-data-already-published-e.html)
“Newly arrived DDBJ data (new data that have arrived after a scheduled DDBJ release)” are data made publicly available on the next day of the deadline or after for the most recent DDBJ release. The deadlines for the most recent releases are listed in the text of [the release notes](https://ddbj.nig.ac.jp/public/ddbj_database/ddbj/ddbjrel.txt). For example, if the most recent release were Release 67, then the deadline would be 8/25/2006, as stated below; thus, in this case, “newly arrived DDBJ data” would be data made publicly available after 8/26/2006.
The present release contains the newest data prepared by the DNA Data Bank ofJapan (DDBJ), GenBank (\*), and European Molecular Biology Laboratory/EuropeanBioinformatics Institute (EMBL/EBI) as of August 25, 2006. (This statement comes from the release notes for Rel. 67; the remainder of that discussion is omitted here.)
These symbols are used to indicate amino acids aligned at the sites marked with the symbol.
“*” indicates perfect alignment.
“:” indicates a site belonging to group exhibiting strong similarity.
“.” indicates a site belonging to a group exhibiting weak similarity.
The criterion for distinguishing strong from weak similarity is as follows: Strong similarity corresponds to a PAM250 MATRIX score between amino acids of greater than 0.5, while weak similarity corresponds to a score of 0.5 or less.
In the README excerpt, the lines horizontally adjacent to the phrases
STA
NEQK
:
indicate the amino-acid groups in cases for which the corresponding symbol is present (These are written using single-character notation for amino acids).
The README file included with the ClustalW source package contains the following text.
---
12.The conservation line output in the clustal format alignment file has been changed.
Three characters are now used:
'*' indicates positions which have a single, fully conserved residue
':' indicates that one of the following 'strong' groups is fully conserved:-
STA
NEQK
NHQK
NDEQ
QHRK
MILV
MILF
HY
FYW
'.' indicates that one of the following 'weaker' groups is fully conserved:-
CSA
ATV
SAG
STNK
STPA
SGND
SNDEQK
NDEQHK
NEQHRK
FVLIM
HFY
These are all the positively scoring groups that occur in the Gonnet
Pam250 matrix. The strong and weak groups are defined as strong score >0.5 and weak
score =<0.5 respectively.
----
In ClustalW, BOOTSTRAP calculations are performed for all analyses. Select [Download Tree File] at the end of the output file to download a .phb file.
Note that .phb files will not be produced if the following combinations of options are chosen for the [FORMAT] and [CLUSTERING] fields of the input form.
The services that exist for communicating information about DDBJ are
as follows. Choose whichever resource is most appropriate for your
purposes.
- [DDBJ Mail Magazine](/subscribe-ddbj-e.html)
- [RSS feed](/data-feed-e.html)
- [Twitter](https://twitter.com/DDBJ_topics)
While no limitations are placed on information citations from the DDBJ website, DDBJ is not responsible for websites that cite information from DDBJ or how the cited information is displayed. When citing information from this website, please clearly indicate that the information has been taken from the DDBJ website.
If possible, please let us know the following information from contact form.
The website on which the information will be cited (or where image(s) will be reproduced)
The DDBJ is a database center of nucleotide sequences, so it does not
distribute any clones.
Please contact the submitter of the clone sequence directly.
When all sequencing data files listed in the Run metadata are uploaded to the DRA server, the "Validate data files" button becomes clickable and users are able to start the validation process.If the button remains inactive after submitting metadata ("metadata_submitted"), check the following points.
All data files listed in the Run metadata have not yet been uploaded.
At this time, it is necessary for submitters to contact the BioProject team to request updates and withdrawals as necessary. Please note that when BioProjects are updated, the submission overview page in the D-way submission portal will not reflect this change. That page is only a record of the initial submission, and does not display changes made in the BioProject database.
No, typically, you should cite the accession numbers that are assigned to your data submissions, e.g. the DDBJ nucleotide sequence or DRA Run accession numbers.
[Which accession numbers should be cited in publication?](/faq/ja/cite-accession.html)
If an individual BioProject needs to be referenced, state that "The data have been deposited with links to BioProject accession number PRJDBxxxxxx in the DDBJ BioProject database." along with the accession numbers assigned to the data submissions.
At this time, it is necessary for submitters to contact the BioSample team to request updates and withdrawals as necessary. Please note that when BioSamples are updated, the submission overview page in the D-way submission portal will not reflect this change. That page is only a record of the initial submission, and does not display changes made in the BioSample database.
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
Since June 2021, when the sequence is less than 100 bp in its length, we will refuse the sequence data submission.
At DDBJ, we do not provide any official services to accept SNV, CGH analysis, microarray, variation and so on. We assume that you can submit your data at NCBI or EBI. Please submit to some of followings. If you have any questions, please ask each database, directly.
To get a FASTA format of WGS, TSA, or TLS entries, please use "getentry", specifying the following values.
ID : Specify the Accession Number. Output format : Select "total nt seq FASTA" for the result. Result : Select one from the following filetype for the output.
html
text
compress (gz)
Limit : Set an upper limit number of the result. When you specify the Limit "0", there is no upper limit of the data acquisition.
For more information about each value, please see getenry HELP.
In the JGA submission, fields including the Subject ID and Gender are required. Specifically, that the main variable (e.g., heart disease) and co-variates (e.g., age, weight) used in the analysis are submitted to JGA so that other people can reproduce the information in your publication. The goal is to include the data that would be required for another researcher to be able to reproduce the published analysis.
DDBJ JGA/NCBI dbGaP/EBI EGA do not exchange data. However, summary metadata of dbGaP and EGA are indexed by the omics metadata cross search system "EBI Omics DI". The JGA summary metadata will be indexed by Omics DI.
For DDBJ nucleotide sequence submission system([NSSS](/ddbj/web-submission-e.html)), 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](/ddbj/web-submission-help-e.html#flow-5-1)
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"](/ddbj/file-format-e.html#sequence).
See also [Wikipedia, FASTA format](https://en.wikipedia.org/wiki/FASTA_format)
When you use DDBJ services in your research, we would appreciate it if you would include [a reference to DDBJ](/faq/en/ddbj-cited-article-e.html) 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".
---
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.
---
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: Mass Submission System (MSS) (click the service name to send an e-mail) Body: (* Required)
About using MSS
・Have you ever used this system for your submission? * Yes / No
In case of either *1 or *2, please take following steps before MSS submission.
Please register your project information in ioProject 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.
**Subject** ： Select from the following items.
- Our paper was publishied
- Our paper was accepted
- Change the hold-date
- Change discription about the contact person
**To** ： [Data updates /
Corrections](mailto:ddbjupdt@ddbj.nig.ac.jp) (click the service name to
send an e-mail)
**Body** :(\* Required)
\[For all subjects\]
: Applicant Name\*
: Applicant Email address\*
: Contact person Name（When you are not contact person, please input
this item.）
: Contact person Email address（When you are not contact person, please
input this item.）
: Accession Numbers\*
\[Our paper was publishied\]
: Paper Title \*
: Paper All authors \*
: Paper Journal \*
: Paper Volume
: Paper Issue
: Paper Start page - End page
: Paper Year
: Paper URL
: Paper PubMed ID
: Paper DOI
\[Our paper was accepted\]
: Paper Title \*
: Paper All authors \*
: PaperJournal \*
: Paper Volume
: Paper Issue
: Paper Start page - End page
: Paper Year
: Paper URL
: Paper PubMed ID
: Paper DOI
: When will you release the data?（Select from the following
items.）\*
- Release immediately
- Specify the hold-date → Please specify the hold-date
\[Change the hold-date\]
: New hold-date（Select from the following
items.）\*
- Release immediately
- Specify the hold-date → Please specify the hold-date
\[Change discription about the contact person\]
: Name ( Current )
: Name ( Update )
: Email address( Current )
: Email address( Update )
: Institution ( Current )
: Institution ( Update )
: Address ( Current )
: Address ( Update )
: Phone ( Current )
: Phone ( Update )
: FAX ( Current )
: FAX ( Update )
\[For all subjects\]
: Message
Mutual data exchange between [NCBI
GEO](https://www.ncbi.nlm.nih.gov/geo/) and
[ArrayExpress](https://www.ebi.ac.uk/arrayexpress/) is not realized so
GEA data are not shared with GEO. ArrayExpress had been imported GEO
data, however, this import was suspended.
BioProject and BioSample registered during GEA submission are exchanged
with NCBI/EBI in the framework of INSDC.
No. Both annotation and sequence files are necessary for an MSS submission. Please visit the following sites for detailed instructions to prepare submission files. Sequence file, Annotation file, Sample annotation file.
In such case, please inform us your D-way account. Then, the submission files can be transferred to a sub directory (usually named ”mass") under your D-way account by scp (File transfer). Please visit the "Data submission to DRA" for how to create a D-way account, if you do not have an account.
For DRA, you may send a metadata summary list attached to the accession number notification e-mail. For sequencing data, download archived fastq files and provide them to reviewers through access-controlled file sharing services or servers.
For JGA, we can not offer the reviewer access service due to the policy.
For open-access GEA/DRA/DDBJ, if you make your data public, all users including reviewers can access the data.
Confirm the following points.
- Authentification is by using SSH key not by password.
- A private key is pair of a public key registered in a D-way account. [Manual](/account-e.html#enable-dra-submission-in-account)
- Make sure to specify a private key for authentification and not a private key for dataset encryption/decryption. [Manual](/jga/download-e.html#data-use-approval-download)
- A private key file has read permission.
- A private key file permission is set as others cannot access. For example, rw-------.
- A passphrase for private key is correctly entered.
- The ssh connection with the port number 443 is allowed in your network (Please ask your network administrator)
When transferring data files by using a private key generated in the other operating system, please check format of a private key. [Convert private key](/account-e.html#convert-private-key)
- In Unix/Mac OS X: Convert a key in the Windows PuTTY file format into the OpenSSH.
- In Windows WinSCP: Convert a key in the Unix/Mac OS X OpenSSH file format into the Windows PuTTY format.
When these are correct, because we do not support technical details regarding use of third-party softwares, please refer to websites of softwares or confirm your system administrators whether ssh (in the case of JGA, port 443) is allowed or not.
Because the [DDBJ Trace Archive](/dta/index-e.html) will be integrated to SRA, we basically do not accept sequencing traces (chromatograms). Please submit fastq files (bases and quality values) to [DRA](/dra/index-e.html) by choosing a Genetic Analyzer series instrument in the DRA Experiment [Instrument Model](/dra/submission-e.html#Instrument).
Please cite the accession numbers that are assigned to your data submissions, e.g. the DDBJ nucleotide sequence or DRA Run accession numbers.
## DRA {#dra}
A DRA submission is composed of following objects with unique prefix.
- **Submission**: DRA
- **BioProject (Study)**: PRJD
- **Experiment**: DRX
- **BioSample (Sample)**: SAMD
- **Run**: DRR
- **Analysis**: DRZ
{% include image.html url="books/sra_object.png" caption="Metadata objects" class="w450" %}
Please cite accession number(s) of objects you want to refer in your publication.
We recommend to cite the DRR Run accession numbers.
## DDBJ {#ddbj}
Cite accession number(s) assigned to nucleotide sequence(s).
[Prefix Letter List](/prefix-e.html)
## GEA {#gea}
Cite Experiment accession "E-GEAD-n".
[GEA Accession](/gea/overview-e.html#acc)
## BioProject {#bioproject}
[Please avoid citing only BioProject accession](/faq/en/project-accession-e.html).
## BioSample {#biosample}
Please avoid citing only BioSample accession.
No, typically, it is appropriate to cite the accession numbers that are assigned to your data submissions, e.g. the DDBJ nucleotide sequence or DRA Run accession numbers.
[Which accession numbers should be cited in publication?](/faq/ja/cite-accession.html)
If an individual BioSample needs to be referenced, state that "BioSample metadata are available in the DDBJ BioSample database under accession number SAMDxxxxxxxx".
If you want to release your data, specify DDBJ/DRA/GEA accession numbers to be released. When only BioProject accession is informed, only the BioProject record is released and related data are not released. Similarly, when only BioSample accession is informed, only the BioSample record is released and related data are not released.
DDBJ/DRA/GEA data release triggers relase of referencing BioProject and BioSample. FAQ: [How are linked BioProject/BioSample/sequence data released?](/faq/en/bp-bs-seq-release-e.html)
## DDBJ {#ddbj}
Inform accession number(s) of nucleotide sequence(s) to be released through the [update form](/ddbj/update-form-e.html).
## DRA {#dra}
Login D-way and [release DRA data by yourself](/dra/submission-e.html#change-hold-date).
## GEA {#gea}
Inform GEA Experiment accession number (E-GEAD-n) or Submission ID (e.g., ESUB000001) to be released through the [contact form](/contact-ddbj.html).
## BioProject {#bioproject}
Inform BioProject accession number (e.g., PRJDB1) or Submission ID (e.g., PSUB000001) to be released through the [contact form](/contact-ddbj.html).
When only BioProject accession is informed, only the BioProject record is released and related data are not released.
## BioSample {#biosample}
Inform BioSample accession number (e.g., SAMD00000001) or Submission ID (e.g., SSUB000001) to be released through the [contact form](/contact-ddbj.html).
When only BioSample accession is informed, only the BioSample record is released and related data are not released.
For sequence data related to the [Barcode of Life project](https://ibol.org/), submit nucletide sequence(s) to [DDBJ](/ddbj/index-e.html).
Because all data in [Trace Archive](https://trace.ncbi.nlm.nih.gov/Traces/trace.cgi?view=list_arrivals) will be migrated to [SRA](https://www.ncbi.nlm.nih.gov/sra), [DDBJ Trace Archive](/dta/index-e.html) no longer accepts trace data.
You may submit fastq files from Sanger-type sequencers to [DRA](/dra/submission-e.html). Submit fastq files and select a Sanger-type sequencer in the Experiment [Instrument Model](/dra/submission-e.html#Instrument).
If you want to submit trace data, please submit them to [NCBI Trace Archive](https://trace.ncbi.nlm.nih.gov/Traces/trace.cgi?view=list_arrivals).
, if necessary. 
