Last updated:2016.11.24.

FAQ

Keyword Search

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

FAQs 31 : Tag = search
Can I confirm previous version of the sequence data? getentry search update

Previous versions of sequence data are available by using getentry webAPI.

See gethistory on getentry HELP.

Last Updated:June 25, 2014
We would like to quote the article of DDBJ. search
When you kindly describe about using DDBJ on academic papers etc., please use the following article.
In general, it is the latest article related to DDBJ on Nucleic Acids Res. Database issue. When you want to know the article about the service of the DDBJ, please refer to How to Use DDBJ.
Last Updated:May 16, 2016
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
How to describe accession numbers on the academic paper? search submission

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)----'.

Last Updated:July 2, 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
What is "Direct Submission" in TITLE of REFERENCE 1? search submission

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.

Last Updated:July 1, 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
Tell us conditions to release unpublished data. search submission
After the specified hold date, I can not find my sequence data. search update

We will check and support it.
Please contact us from contact form by selecting the item, "Updating Submitted Data" with accession numbers.

See Principle of "Hold-Until-Published" data release.
If your data was submitted before 1998, it might be still unpublished after hold date.

If the information of contact person is old or invalid, we may be unable to acknowledge publication of the data or any other important announcement.
See the relevant item in Data Updates/Corrections and contact us from this form to send request by selecting the subject, "Change the contact person, belonging, institution, etc..".

Last Updated:July 3, 2014
Why is the retracted data still available? search submission

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.

Last Updated:August 4, 2016
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・PMID
Last Updated:July 3, 2014
What is the search service that the latest data are available at the earliest period? getentry search

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.

Last Updated:June 25, 2014
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 long are the temporal differences of data releases among DDBJ, EMBL-Bank and GenBank? search

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.

Last Updated:June 8, 2015
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
Regarding the phrase “after a scheduled DDBJ release”: When, specifically, does this phrase describe? ARSA getentry search
“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. 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.)
Last Updated:June 15, 2015
I did not obtain the search results that I was expecting. Did I make a mistake in conducting my search? ARSA BLAST getentry search
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.
Last Updated:June 8, 2015
Does DDBJ offer data search and analysis services? analysis search
There are two ways of searching and analyzing data, as discussed below. Please select the option that is appropriate for your needs.
  • 1. Conducting searches and analyses using a network server such as an FTP or web server.
    You may access these networking tools via Search / Analysis.  
  • 2. Conducting searches and analyses by logging in to the supercomputer system at the National Institute of Genetics (NIG).
    (This requires a supercomputer user ID. You will need to sign up for a new user account on the NIG supercomputer system.)
Last Updated:June 15, 2015
What format should I use when including results obtained with DDBJ search and analysis software in a journal publication? search
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 How to Use DDBJ Reference about the original papers and other related papers on the DDBJ search and analysis software.
Last Updated:April 13, 2016
Where can I find the original papers and other related papers on the DDBJ search and analysis software? BLAST ClustalW search
Please see the DDBJ home page How to Use DDBJ Reference.
Last Updated:April 13, 2016
Is it possible to view search results at a later time? BLAST search
Search results may be accessed via the following URL, which contains a Request ID field.
http://blast.ddbj.nig.ac.jp/blast/r/Request ID
Request ID
Note that the Request ID will be displayed in the window that appears after transmitting the input. Make sure to note down this.
Input content post-transmission window
Search results display window
Reading period
Search results may be viewed up to 7 days after the execution of the search.
Last Updated:June 4, 2015
How do I interpret the search results? BLAST search
Search results are displayed in the following order.
  1. Precedence table of sequences with high homology scores
  2. Homologous sequences and their alignment
  3. 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.

BLAST Reference
Last Updated:June 4, 2015
A portion of the sequence that I entered was replaced with [N](X)! What happened? BLAST search
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 “Filtering” 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.
Last Updated:June 3, 2015
Is there a way to link directly to data (accession numbers) registered in the DDBJ? getentry search
Last Updated:June 8, 2015
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
Regarding the E value displayed in the BLAST analysis results: How is this value calculated? BLAST search
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.
Last Updated:April 13, 2017
What rules govern the order in which BLAST search results are displayed? BLAST search
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.
Last Updated:June 1, 2015
The number of search results shown is too small! (I receive the message “No hit found.”) BLAST search
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.
Last Updated:June 1, 2015
How do I get a FASTA format of TSA or WGS entries? getentry search

To get a FASTA format of TSA or WGS 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.

Please see the following video as well.

Last Updated:May 19, 2016
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