DDBJ flat file format

DDBJ (DNA Data Bank of Japan) shares annotated/assembled nucleotide sequence data as a member of INSDC (International Nucleotide Sequence Database Collaboration).
For the sharing purpose, DDBJ collects the nucleotide sequences experimentally determined, and constructs the database in accordance with the rule agreed with INSDC.

The database also includes the data from Japan Patent Office (JPO), European Patent Office (EPO), United States Patent and Trademark Office (USPTO), and Korean Intellectual Property Office (KIPO).

The database is a collection of “entry” which is the unit of the data.
The entry submitted to DDBJ is processed and publicized according to the DDBJ format for distribution (flat file).
The flat file includes the sequence and the information of submitters, references, source organisms, and “feature” information, etc.
The “feature” is defined by The DDBJ/ENA/GenBank Feature Table Definition to describe the biological nature such as gene function and other property of the nucleotide sequence.

The virtual sample of DDBJ flat file

LOCUS       AB000000              450 bp    mRNA    linear   HUM 01-JUN-2009
DEFINITION  Homo sapiens GAPD mRNA for glyceraldehyde-3-phosphate
            dehydrogenase, partial cds.
ACCESSION   AB000000
VERSION     AB000000.1
KEYWORDS    .
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 450)
  AUTHORS   Mishima,H. and Shizuoka,T.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-NOV-2008) to the DDBJ/EMBL/GenBank databases.
            Contact:Hanako Mishima
            National Institute of Genetics, DNA Data Bank of Japan; Yata 1111,
            Mishima, Shizuoka 411-8540, Japan
REFERENCE   2
  AUTHORS   Mishima,H., Shizuoka,T. and Fuji,I.
  TITLE     Glyceraldehyde-3-phosphate dehydrogenase expressed in human liver
  JOURNAL   Unpublished (2009)
COMMENT     Human cDNA sequencing project.
FEATURES             Location/Qualifiers
     source          1..450
                     /chromosome="12"
                     /clone="GT200015"
                     /collection_date="2007"
                     /db_xref="taxon:9606"
                     /geo_loc_name="Japan"
                     /map="12p13"
                     /mol_type="mRNA"
                     /organism="Homo sapiens"
                     /tissue_type="liver"
     CDS             86..>450
                     /codon_start=1
                     /gene="GAPD"
                     /product="glyceraldehyde-3-phosphate dehydrogenase"
                     /protein_id="BAA12345.1"
                     /transl_table=1
                     /translation="MAKIKIGINGFGRIGRLVARVALQSDDVELVAVNDPFITTDYMT
                     YMFKYDTVHGQWKHHEVKVKDSKTLLFGEKEVTVFGCRNPKEIPWGETSAEFVVEYTG
                     VFTDKDKAVAQLKGGAKKV"
BASE COUNT          102 a          119 c          131 g           98 t
ORIGIN
        1 cccacgcgtc cggtcgcatc gcacttgtag ctctcgaccc ccgcatctca tccctcctct
       61 cgcttagttc agatcgaaat cgcaaatggc gaagattaag atcgggatca atgggttcgg
      121 gaggatcggg aggctcgtgg ccagggtggc cctgcagagc gacgacgtcg agctcgtcgc
      181 cgtcaacgac cccttcatca ccaccgacta catgacatac atgttcaagt atgacactgt
      241 gcacggccag tggaagcatc atgaggttaa ggtgaaggac tccaagaccc ttctcttcgg
      301 tgagaaggag gtcaccgtgt tcggctgcag gaaccctaag gagatcccat ggggtgagac
      361 tagcgctgag tttgttgtgg agtacactgg tgttttcact gacaaggaca aggccgttgc
      421 tcaacttaag ggtggtgcta agaaggtctg
//

Flat file displays the information provided by submitters with DDBJ format.
Even when the sequences are similar, the contents on the flat files may vary according to the submitter’s research aim etc.
Please take that point into consideration when you refer search results.

FIELD COMMENTS

locus name, sequence length, molecule type, molecular form, division, the date of last release

Locus name is a unique ID of the entry in the database. In DDBJ, since July 1996, the locus name has been assigned the same asaccession number.

Notice: No information is available on the Master record of MGA data.

According to the value of /mol_type qqualifier for source feature, it is described as DNA, RNA, mRNA, rRNA, tRNA, or cRNA.

This column indicates whether molecular form of nucleotide sequence is “linear” or “circular”. If the entry is the full length of circular form, “circular” is appeared.

DDBJ classifies entries into 21 divisions as below;

a: taxonomic divisions

b: other divisions

The current publicized date is described. If the entry is updated and reopened to public site, this date will be changed.

The definition briefly describes the information of gene(s). “DEFINITION” is constructed by each of the three data banks in accordance with standard rules in principle.
However, in the case of EST or GSS submission using Mass Submission System, DDBJ will sometimes ask submitters to construct “DEFINITION”.

[Sample]

Complete sequence of maize catalase coding gene

  DEFINITION  Zea mays Cat3 gene for catalase, complete cds.

Format: [organism name] [gene name] gene for [product name], complete cds.

• organism name: The scientific name is indicated as the organism name, in principle.
• gene name: the symbol of the gene
• product name: the general name of product
• complete cds: this coding sequence is complete

Partial sequence of human glyceraldehyde-3-phosphate dehydrogenase coding cDNA

  DEFINITION  Homo sapiens mRNA for glyceraldehyde-3-phosphate 
              dehydrogenase, partial cds.

Format: [organism name] mRNA for [product name], partial cds.

• partial cds: this protein coding sequence is partial
• The gene name is omitted, because the submitter did not describe.

Partial sequence of Bacillus 16S rRNA

  DEFINITION  Bacillus sp. AZ25 gene for 16S rRNA, partial 
              sequence.

Format: [organism name] [strain name] gene for [product name], partial sequence.

• In cases of unidentified species, comparison of intraspecies, and so on, describe name of strain, isolate or some, as identifier.
• partial sequence: this sequence is part of 16S rRNA.

Multiple CDS of rat mitochondrial DNA

  DEFINITION  Rattus norvegicus mitochondrial genes for cytochrome 
              c oxidase subunit II, ATPase subunit 6, cytochrome c 
              oxidase subunit III, partial and complete cds.

Format: [organism name] [gene name 1], [gene name 2], …. genes for [product name 1], [product name 2], ….. , partial and complete cds.

• The gene names and/or product names are subsequently described from 5’to 3’ end.
• “partial, complete and partial cds” is abbreviated to “partial and complete cds”.
• If some genes have only gene names or product names, only gene name or product name is described principally.
• If the “DEFINITION” is too long, some information, such as map position, is described instead of the gene or product names.
• Sometimes gene cluster or operon name is described, if it is considered reasonable.

EST data of human liver 3’ end

  DEFINITION  Homo sapiens cDNA, clone:ABC123, 3' end, expressed 
              in liver.

Format: [organism name] cDNA, clone:[clone name], [other information].

• The clone name is mandatory.

GSS data of mouse chromosome 1q

  DEFINITION  Mus musculus DNA, clone:1H11A14, 1q region.

Format: [organism name] DNA, clone:[clone name], [other information].

• The clone name is mandatory.

TPA (Third Party Data) of human GAPD

  DEFINITION  TPA_exp: Homo sapiens GAPD mRNA forglyceraldehyde-3-phosphate 
              dehydrogenase, complete cds.

Format: [TPA header]: [organism name] [gene name] mRNA for [product name], complete cds.

• In the case of TPA (Third Party data), either of “TPA_exp” (for TPA:experimental) or “TPA_inf” (for TPA:inferential) is described at the beginning of DEFINITION.

This line shows accession number of the entry data.

Conventional sequence data

A unique accession number is issued to the data submitter by each of the three data banks. The accession number is composed of 1 alphabet character and 5 digits (ex. A12345) or 2 alphabet characters and 6 digits (ex. AB123456). The former style was used in 1980s, but later the latter style was introduced because of data explosion.
The alphabet part is called “prefix”. Please refer the prefix list.

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. You can find the same updated entry with both the primary and the secondary accession numbers.

  ACCESSION   AB999999 AB888888 AB777777

Bulk sequence data; WGS, TSA, TLS

The accession number assigned to each entry of WGS, TSA and TLS data consists of 4 alphabet characters and 8 (sometimes 9 or 10, if necessary) digits.
The alphabet part is called prefix.
See also For Large Scale Data (four prefix).
Example:ZZZZ01000001

ZZZZ (4 letters)	Prefix to distinguish each project, project_id
01 (2 digits)	Version number of the data set, set_version
000001 (6 digits)	ID of each individual sequence (It might be 7 or 8 digits depended on the number of entries.)

The set_version goes up for every update of the dataset. Example:ZZZZ02000001

  ACCESSION   ZZZZ01000001 ZZZZ01000000

For MGA data

This (ACEESSION) line shows a number assigned by INSDC to a resource.

The number is composed of 5 alphabet characters and 7 digits (ex. ABCDE0000001).An accession number assigned to an entry of a resource units is displayed in the MGA lines.

Example:ABCDE0000001

AB (first two characters) identi	identifier to each project.
CDE (third to fifth characters)	identifier to each of resources on each project.
0000001 (7 digit numeric numbers)	number for each sequence entry in a resource.

*1 The information about each project id is avilable at the project_index page.
*2 “resource” here means a unit of identical origin, such as tissue, cells, from which sequence are obtained.

  ACCESSION   ZZZZZ0000000

This line consists of an accession number and a version number, like “AB123456.1”, in which the digit(s) after the period is a version number.

The data open to public for the first time is version number as “1”. The reason for adding VERSION is that since a released sequence sometimes revised by the submitter, the accession number alone cannot specify the sequence in question causing the user a trouble. The number is increased by one every time when a revised sequence is made public. And accession number will NOT be changed generally.

  VERSION      AB000000.1

For MGA data

This line consists of a number assigned to a resources unit in which the digit(s) after the period is a version number.
Since the sequence of an MGA entry is not allowed to update, the version number has to be “1”.

  VERSION    ZZZZZ0000000.1

The DBLINK line is used to link other databases for BioProject, BioSample accession numbers, Sequence Read Archive Run accession numbers and so on.

DDBJ has replaced the PROJECT line by DBLINK line format since 2009 to expand for other data resources than projects.

DBLINK      BioProject:PRJDA12345
            BioSample:SAMD01234567
            Sequence Read Archive:DRR012345, DRR012346     

The KEYWORDS lines were used for indexing (gene) and (product) names in the past.

For now, KEYWORDS lines are used to indicate the detail category of the data (EST, TSA, HTC, HTG, GSS, WGS, TPA etc) information about experimental method, “finishing level” of genome sequencing and else, if necessary. See also INSDC agreed methodological keywords.

This line shows the scientific name (and common name, if defined) on organism from which the sequence is obtained and an organelle type if the sequence is derived from an organelle other than the nucleus.

SOURCE      Homo sapiens (human)

The organism name and its phylogenic lineage from which the sequence is obtained are described.

The scientific name is indicated as the organism name in 1st line. If the sequence is obtained from an unidentified organism or artificially synthesized, the name registered on the Unified Taxonomy Database is described instead of scientific name.

The phylogenic lineage information based on the Unified Taxonomy Database is started from 2nd line.

  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi
            Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.

The information of submitter(s) is described as REFERENCE 1 (except old entries and some CON entries).

In the case of Nucleotide Sequence Submission System, REFERENCE 1 is processed with the information entered on “Contact person” and “Submitter” pages. In the case of Mass Submission System, REFERENCE 1 is processed with the information entered in annotation file.

REFERENCE   1   (bases 1 to 450)

Notice: The portion, “(bases 1 to 450)”, is not available on the Master record of MGA data.

Submitter(s) of the entry is/are indicated in principle. Submitter is responsible for the data and can update it.

  AUTHORS   Mishima,H. and Shizuoka,T.

“Direct Submission” is indicated to follow the standard form.

  TITLE     Direct Submission

At first, “Accept Date” of the entry is indicated. “Accept Date” is defined as the date when DDBJ have received the acceptable data to assign accession number in principle. Even if the entry is updated, “Accept Date” is NOT changed. Then, the information about the address and the affiliation of “Contact Person” is indicated.

  JOURNAL   Submitted (30-NOV-2008) to the DDBJ/EMBL/GenBank databases.
            Contact:Hanako Mishima
            National Institute of Genetics, DNA Data Bank of Japan; Yata 1111,
            Mishima, Shizuoka 411-8540, Japan

E-mail address, phone & fax nos.

• To follow the Japanese law of protecting personal information, DDBJ will delete both phone and fax numbers, and E-mail address from the flat files of the entries submitted to DDBJ.However, if you wish to disclose any of the three items, please contact us with contact form,?specifying the item(s) to be disclosed.
• If you wish to contact the submitter(s) of an entry of your interest, please contact us via the contact form by selecting ‘Inquiry to the sequence submitters’ and briefly stating your reason (e.g., requesting the transfer of cloned sequences, etc.). We will then forward your message to the submitter(s).

Phone and fax numbers and E-mail address are deleted.

  JOURNAL   Submitted (30-NOV-2000) to the DDBJ/EMBL/GenBank databases.
            Contact:Hanako Mishima
            National Institute of Genetics, DNA Data Bank of Japan; Yata 1111,
            Mishima, Shizuoka 411-8540, Japan

When the submitters wish to keep their contact information disclosed, it will be described as,

  JOURNAL   Submitted (30-NOV-2000) to the DDBJ/EMBL/GenBank databases.
            Contact:Hanako Mishima
            National Institute of Genetics, DNA Data Bank of Japan; Yata 1111,
            Mishima, Shizuoka 411-8540, Japan
            E-mail :mishima@supernig.nig.ac.jp
            Phone  :81-55-981-6853
            Fax    :81-55-981-6849

The information of references related to the submitted sequence is indicated on REFERENCE line (other than (REFERENCE 1). Since REFERENCE 2 indicates the publication status of the sequence, the reference which does not describe about the submitting sequence is indicated as REFERENCE 3 or after, not as REFERENCE 2.

When DDBJ notices a paper publication with an accession number, DDBJ will update the entry with the accession number, if necessary. During the process of the update, the prepublication paper(s) described in the line(s), REFERENCE 2 and/or later, will be revised without any notice to submitters, if applicable; i.e. When the submitted data, submitters’ affiliation, author names, title, and journal name of the prepublication paper, are enough reasonable to be revised.

In the cases of the manuscript in preparation, submitted for publication, in press, or published

  REFERENCE   2
    AUTHORS   Mishima,H., Shizuoka,T. and Fuji,I.
    TITLE     Glyceraldehyde-3-phosphate dehydrogenase expressed in human liver
    JOURNAL   Unpublished (2009)

In the case of no schedule for publication except the international nucleotide database.

  REFERENCE   2
    AUTHORS   Mishima,H., Shizuoka,T. and Fuji,I.
    TITLE     Glyceraldehyde-3-phosphate dehydrogenase expressed in human liver
    JOURNAL   Published Only in Database(2009)

The information about an entry that can not be described using FEATURES or the other fields. For instance, if submitter has the other affiliation to REFERENCE 1, it can be described on COMMENT line.

  COMMENT     Human cDNA sequencing project.

Structured COMMENT

Structured COMMENT is a format to describe and to share some datasets undefined in feature/qualifier.
SUsing structured COMMENTs, datasets can be shared via flatfiles of INSDC in the community of submitters and users.
To describe structured COMMENT, the dataset is required to be describe in structured sets of [names of items] and [values of items] on COMMENT line.
There are some predetermined formats of structured COMMENTs that are required to submit some kinds of sequence data derived from genome projects (includingWGS, transcriptome projects (including TSA) and so on.

  COMMENT     ##Genome-Assembly-Data-START##
              Finishing Goal           :: Finished
              Current Finishing Status :: High Quality Draft
              Assembly Method          :: Newbler v. 2.3
              Genome Coverage          :: 30x
              Sequencing Technology    :: 454 GS Junior; Illumina GA II
              ##Genome-Assembly-Data-END##

:
The above example is an additional information, “Genome-Assembly-Data”, that is required for genome projects.
The contents between ##Genome-Assembly-Data-START## and ##Genome-Assembly-Data-END## are delimited item names and their values by “ :: “.

For MGA data

For MGA Submission, the process for obtaining the submitted sequence data e.g.; (methods for preparing sequences from tissues or cells and processing the sequences for submission) is described.

  COMMENT     The CAGE (cap analysis gene expression) is based on preparation
              and sequencing of concatamers of DNA tags deriving from the
              initial 20/21 nucleotides from 5' end mRNAs.
              Full-length cDNAs were at first selected with the Cap-Trapper
              method. Then, a specific linker (Linker1, some linker contain 5 bp
              sequences that have 15 variations for each rna sample) containing
              the ClassIIs restriction enzyme site MmeI was then ligated to the
              single-strand cDNA and then the second strand of cDNA synthesized.
              The resulting double-stranded cDNA was cleaved by the restriction
              enzyme MmeI and a second linker (Linker2) was ligated to the 2 bp
              overhang at the MmeI cleaved site, to produce a 5' 20/21 tag
              having two linkers at both sides. The ligation products were
              separated from unmodified DNA with magnetic beads. The 5' end cDNA
              tags were released from the beads, and the DNA fragments were
              amplified in a PCR step by using the two linker-specific primers
              (Primer1 (uni-PCR), Primer2 (MmeI-PCR)). The desired 32-37 bp tags
              were purified and ligated to form concatamers, and then the
              concatamer were fractionated and ligated to the plasmid ZErO-2.
              The ligations were finally electroporated into DH10b cells
              (Invitrogen) and obtained plasmids were sequenced with forward
              primers.
              CAGE libraries were sequenced with forward primers essentially as
              described with minor modifications to use zeocin for selection of
              recombinants. We used in-house developed algorithms for the
              extraction of tags and for masking the vectors. CAGE tags were
              extracted with the following parameters: vector masking, minimum
              12 bp recognition allowed; linker (13 bp) masking: maximum
              mismatch, 2 bp allowed; XmaJI site maximum mismatch, 2 bp allowed;
              tag length, 17-24 bp.
              Linker1: "Upper oligonucleotide GN6":
              biotin-agagagagacctcgagtaactataacggtcctaaggtagcgacctagg (5 bp)
              tccgacGNNNNN and "Upper oligonucleotide N6":

Biological features of a submitted sequence data are described with “Feature” key (the biological nature of the annotated feature), “Location” (the region of the sequence which corresponds to Feature), and “Qualifier” (supplementary information about Feature). In principle, EST or GSS entries are not described with any features except the “source” key.

FEATURES are indicated on the basis of the information provided by submitter and modified by databanks to describe the appropriate annotation. The rules of feature description agreed with three databanks are explained at The DDBJ/ENA/GenBank Feature Table Definition in detail.

Feature keys are briefly classified into 3 groups;

• group 1: biological source of the sequence (source)
  The feature, “source” (group 1) is mandatory for all entries in the international nucleotide database.
  The qualifiers “/organism” and “/mol_type” are mandatory for source feature.
• group 2: biological function features of the region
  Feature keys in group 2 fall into families which are in some sense similar in function and which are annotated in a similar manner.A functional family may have a “generic” or miscellaneous key, which can be recognized by the ‘misc_’ prefix, that can used for instances not covered by the other defined keys of that group.
  e.g. CDS, rRNA, etc.
• group 3: difference and/or change of the sequence data
  e.g. variation, conflict, etc.

One of the most frequently used feature key is “CDS” to describe coding sequence for protein. See also CDS feature page.

FEATURES             Location/Qualifiers
     source          1..450
                     /chromosome="12"
                     /clone="GT200015"
                     /collection_date="2007"
                     /db_xref="taxon:9606"
                     /geo_loc_name="Japan"
                     /map="12p13"
                     /mol_type="mRNA"
                     /organism="Homo sapiens"
                     /tissue_type="liver"
     CDS             86..>450
                     /codon_start=1
                     /gene="GAPD"
                     /product="glyceraldehyde-3-phosphate dehydrogenase"
                     /protein_id="BAA12345.1"
                     /transl_table=1
                     /translation="MAKIKIGINGFGRIGRLVARVALQSDDVELVAVNDPFITTDYMT
                     YMFKYDTVHGQWKHHEVKVKDSKTLLFGEKEVTVFGCRNPKEIPWGETSAEFVVEYTG
                     VFTDKDKAVAQLKGGAKKV"

Identifies the biological source of the specified span of the sequence.

Coding sequence; sequence of nucleotides that corresponds with the sequence of amino acids in a protein (location includes stop codon).

”//” is the terminal symbol of the entry.