DDBJ Center News Archive

News from 2013

DDBJ Rel. 95.0, DAD Rel. 65.0 Completed

2013年12月26日

DDBJ Rel. 95.0

DAD (DDBJ amino acid database) Rel. 65.0
  • Date: Sep. 18, 2013
  • 29,553,914entries     8,770,768,717 aa (total number of residues)
  • DAD Release Note
Services: ddbj Keywords: Data Release

PDB 2013-12-21 released

December 26,2013

PDB 2013-12-21 was released.

Services: ddbj Keywords: Data Release

Release of GSS data of soybean (Glycine max)

December 24,2013

DDBJ released GSS data of soybean (Glycine max), which had been submitted by National Institute of Agrobiological Sciences.

Reference; DAIZUbase

The accession numbers are as follows. They are available on getentry.

    GSS: LB000001-LB184894 (184,894 entries)

Services: ddbj Keywords: Data Release

Release of genome sequence data of carnation (Dianthus caryophyllus)

December 20,2013

DDBJ released genome sequence data of carnation (Dianthus caryophyllus), which had been submitted by Kazusa DNA Research Institute.

Reference; Carnation DB

The accession numbers are as follows. They are available on getentry or DRASearch.

    scaffold CON: DF340864-DF357213 (16,350 entries)
    WGS: BAUD01000001-BAUD01089083 (BAUD.gz) (89,083 entries)
    raw data: DRR014087-DRR014092

Services: ddbj Keywords: Data Release

Changes in organism strain information management

December 13,2013

INSDC members assign strain-level taxonomy IDs to microbes whose genomes are submitted to the INSDC. The INSDC is, however, going to stop assigning strain-level taxonomy ID in February, 2014, and BioSample IDs will be defined microbial genomes instead of strain-level taxonomy ID.

For more details, please refer to "Planned change in bacterial strain-level information management".

Taxonomy

Assigning strain-level TaxID will be discontinued in February 2014. However, existing strain-level TaxIDs will remain, and we will continue to add informal strain-specific names for genomes from specimens that have not yet been identified to the species level.

If a genome assembly is derived from an unidentified/unpublished organism, species-level informal names will still be generated which use strain identifiers in form of "Genus sp. strain".

BioSample

DDBJ Center will start to accept new BioSample submissions in February 2014. Submitters of genome sequences will be required to register sample metadata in the BioSample database for each organism that they are sequencing. The BioSample submission will include the strain information and other metadata, such as culture collection and isolation information, as appropriate.

BioProject

Submitters of genome sequences are already required to register metadata about the research project in the BioProject database. We no longer require a one-to-one relationship between a BioProject accession and a genome. Instead, a research effort examining multiple strains of a species or multiple species of drug-resistant bacteria, for example, could be registered as a single BioProject.

Strain-level Taxonomy ID to BioSample ID
Services: biosample Keywords:

UniProt 2013_12 released

December 13,2013

UniProt 2013_12 was released.

Services: ddbj Keywords: Data Release

PDB 2013-12-07 released

December 13,2013

PDB 2013-12-07 was released.

Services: ddbj Keywords: Data Release

Apology for the trouble of browsing and downloading DDBJ’s anonymous FTP

December 11,2013

In relation to NIG SuperComputer system maintenance of last week-end, the trouble of browsing and downloading DDBJ’s anonymous FTP occured as follows.

  • Date&Time: December 9, 2013 at 0:00 - 18:00 (JST)
  • Troubled directory: ftp://ftp.ddbj.nig.ac.jp/ddbj_database
  • Problem:browsing and downloading is unavailable in the target directory

As of Dec. 11 (Tue ) 12:00 (JST), the trouble was already fixed .
DDBJ sincerely apologizes for your inconveniences.
Services: ddbj Keywords: Maintenance

Suspension of the DDBJ activity during the New Year Holidays

December 11,2013
We at DDBJ will temporally close our office during the New Year Holidays, in observance of the Japanese custom, New DDBJ Nucleotide Sequence Submission System and data release are also closed.
However, the computer search/analysis and FTP are available as usual.

Web form posting and E-mail sending for inquiries of data submission, data update, search/analysis, supercomputer account application, D-way system, etc., are available throughout the holidays. But, please note in advance that replies from DDBJ is after the reopening of the office in January, 2014.[make_table set_width=650px title_font_weight=normal zebra=yes zebra_color=#efece5]DDBJ office close:Dec. 28(Sat), 2013 - Jan. 5(Sun), 2014     New DDBJ Nucleotide
    Sequence Submission System:Dec. 26(Thu), 2013 at 17:00(JST)
     - Jan. 6(Mon), 2014 at 12:00(JST)Data release suspensionDec. 26(Thu), 2013 - Jan. 6(Mon), 2014 Reply for inquiries
(submission, search/analysis, supercomputer):Dec. 28(Sat), 2013 - Jan. 5(Sun), 2014    DRA/BioProject Accession No. issue :Dec. 28(Sat), 2013 - Jan. 5(Sun), 2014    [/make_table]Thank you for your understanding and cooperation.
December 11, 2013     DDBJ
Services: ddbj Keywords: Announcement

HOLIDAY CLOSING NOTICE

December 10,2013
Please be informed that, for the new year's holidays, we will be closing from 28th Dec. 2013 until 5th Jan. 2014.
After the holiday period, we will begin replying to inquiries and resume issuing accession numbers. During this period, however, we will continue to accept online submissions via D-way and searches for DRA and BioProject.
We regret any inconvenience this may cause and appreciate your kind understanding.
Services: bioproject,biosample,gea,dra,dta,jga Keywords: Announcement

Release of GSS data of false killer whale (Pseudorca crassidens)

December 09,2013

DDBJ released GSS data of false killer whale (Pseudorca crassidens), which had been submitted by National Institute of Genetics.

The accession numbers are as follows. They are available on getentry.

    GSS: DE737776-DE827431 (89,656 entries)

Services: ddbj Keywords: Announcement

(Dec. 6-9) NIG SuperComputer and DDBJ network services will be unavailable

November 29,2013
NIG SuperComputer and DDBJ network services will be unavailable because of the electric construction of NIG SuperComputer System. Schedule is as follows:
ServicesScheduled (JST)
·D-way·DRA Search·BioProject SearchDec. 6 (Fri) 13:00 - Dec. 9 (Mon) 9:00
·NIG SuperComputer·DDBJ HP·DDBJ anonymous FTP·getentry·ARSA·DDBJ Nucleotide Sequence Submission System·BLAST·ClustalW·DDBJ Read Annotation PipelineDec. 7 (Sat) 17:00 - Dec. 08 (Sun) 24:00

Thank you for your cooperation and understanding.
Services: ddbj Keywords: Maintenance

System temporarily unavailable

November 28,2013
From 13:00 on December 6th (Fri) to 13:00 on December 9th (Mon), DRA and BioProject submission and search services will be unavailable due to system maintenance.
Services: bioproject,biosample,gea,dra,dta,jga Keywords: Maintenance

Release of genome sequence data of strawberries (Fragaria x ananassa and other 4 species)

November 28,2013

DDBJ released genome sequence data of strawberries (Fragaria x ananassa and other 4 species), which had been submitted by Kazusa DNA Research Institute.

Reference; Strawberry GARDEN

The accession numbers are as follows. They are available on getentry and DRASearch.

species WGS scaffold CON SRA
Fragaria x ananassa
(assembled to eliminate heterozygous)
BATS01000001-BATS01220286 (BATS.gz) DF266822-DF269452 DRR013866-DRR013871
DRR013873-DRR013882
Fragaria x ananassa
(assembled with octoploidity)
BATT01000001-BATT01714282 (BATT.gz) DF269453-DF338599 DRR013873-DRR013882
Fragaria iinumae BATU01000001-BATU01118549 (BATU.gz) DF338600-DF339317 DRR013884
Fragaria nipponica BATV01000001-BATV01215530 (BATV.gz) DF339318-DF339818 DRR013885
Fragaria nubicola BATW01000001-BATW01211274 (BATWgz) DF339819-DF340307 DRR013883
Fragaria orientalis BATX01000001-BATX01323675 (BATX.gz) DF340308-DF340817 DRR013886
Services: ddbj Keywords: Data Release

Apology for the trouble of browsing the DDBJ's web services

November 22,2013

From Nov. 20 (Wed) at 20:17 to Nov. 21 (Thu) at 09:32 (JST),in the following DDBJ services, browsing the web page was unavailable. 

  • DDBJ HP
  • D-way
  • DDBJ Nucleotide Sequence Submission System
  • VecScreen
  • getentry
  • ARSA
  • BLAST
  • ClustalW
  • DDBJ Read Annotation Pipeline
  • MiGAP
  • MiGAP-OLD
  • NIG SuperComputer


As of Nov.22 (Fri) (JST), the trouble was fixed in the all services.DDBJ sincerely apologizes for your inconveniences.
Services: ddbj Keywords: Maintenance

UniProt 2013_11 released

November 15,2013

UniProt 2013_11 was released.

Services: ddbj Keywords: Data Release

PDB 2013-11-09 released

November 14,2013

PDB 2013-11-09 was released.

Services: ddbj Keywords: Data Release

PDB 2013-11-02 released

November 07,2013

PDB 2013-11-02 was released.

Services: ddbj Keywords: Data Release

Feature Table: Definition revised

November 05,2013

The DDBJ/EMBL/GenBank Feature Table: Definition is the common annotation manual among the three banks (DDBJ, EMBL-Bank, GenBank) for the construction of the DDBJ/EMBL/GenBank International Nucleotide Sequence Database.
It was revised to version 10.3 in October 2013.

Services: ddbj Keywords: Announcement

Updated tools and documents related to Mass Submission System (MSS)

November 01,2013

DDBJ updated tools and documents related to Mass Submission System.

  • Mass Submission System Making Files Opened
  • Mass Submission System User's Guide (in PDF format) Terminated
  • Utilities for MSS file Error check (UME) V1.32 Released
  • Parser V6.46 Released
  • transChecker V2.13 Released

After the updates, the tools would be compatible with Java Runtime Environment version 1.7 or later.
See DDBJ Mass Submission in detail.

Services: ddbj Keywords: Announcement

PDB 2013-10-26 released

October 31,2013

PDB 2013-10-26 was released.

Services: ddbj Keywords: Data Release

(Nov. 7-12) DDBJ network services will be unavailable for power outage of the NIG

October 31,2013
DDBJ network services will be unavailable because of the electric power outage of the NIG(National Institute of Genetics) and maintenance of the NIG SuperComputer. Schedule is as follows:
ServicesScheduled (JST)
·D-way·DRA Search·BioProject SearchNov. 7 (Thu) 13:00 - Nov. 12 (Tue) 9:00
·NIG SuperComputer·DDBJ HP·DDBJ anonymous FTP·getentry·ARSA·DDBJ Nucleotide Sequence Submission System·BLAST·ClustalW·DDBJ Read Annotation PipelineNov. 8 (Fri) 9:00 - Nov. 11 (Mon) 12:00

Thank you for your cooperation and understanding.
Services: ddbj Keywords: Maintenance

System temporarily unavailable

October 24,2013
From 13:00, Nov 7th (Thu) to 9:00, Nov 12th (Tue), submission and search services of DRA and BioProject will be unavailable due to the inspection work of NIG.
Services: bioproject,biosample,gea,dra,dta,jga Keywords: Maintenance

Submission Restart for Korean Intellectual Property Office (KIPO) data

October 23,2013
Data submission of Korean Intellectual Property Office (KIPO) was restarted. DDBJ distributed 78368 entries of nucleotide sequence data and 47582 entries of amino acid sequence data.

[KIPO data summary]
1) Accession number

 Nucleotide sequence data (78,368 entries): DI168563-DI246930
 Amino acid sequence data (47,582 entries): DI613600-DI661181


2) Data Example
Please check KIPO data example at following URL.
 Nucleotide sequence data:
 http://getentry.ddbj.nig.ac.jp/getentry/na/DI168563

 Amino acid sequence data:
 http://getentry.ddbj.nig.ac.jp/getentry/aa/DI613600

3) Summary of Flat File (FF) structure for KIPO data
3-1: Patent number

KIPO patent number is described by Application and Publication number from this time submission. Therefore, KIPO data can be retrieved by both patent number.

DEFINITION, KEYWORDS and JOURNAL lines were set Publication number with Sequence number as [Publication number]-A/[Sequence number] format (Example: KR 1020100119005-A/1) on KIPO's FF.

Application number is described on AN line at COMMENT Block.

3-2: Header and description on COMMENT Block
Please check the description of each line.
 -----------------------------------------------------------------
   KN  Sequence ID
   AN  Application number
   AD  Application date
   PN  Publication number
   PD  Publication date
   AT  Application title
   AI  Inventors (bar-separated)
   AA  Applicants (bar-separated)
   PR  Priority number=Priority date (bar-separated)
   OS  Organism name
   TY  Sequence type (DNA, PRT)*
 -----------------------------------------------------------------
  *DNA=Nucleotide sequence data, PRT=Amino acid sequence data
4) KIPO submission files
Submission files were processed and submitted to DDBJ by Dr. Byungwook Lee at Korean Bioinformation Center (KOBIC) in collaboration with KIPO.
Services: ddbj Keywords: Announcement

FTP download temporarily unavailable

October 23,2013
From 10:00 to 11:00, 23rd (Wed) Oct., FTP download service will be unavailable due to system maintenance.
Services: bioproject,biosample,gea,dra,dta,jga Keywords: Maintenance

UniProt 2013_10, PDB 2013-10-12 released

October 21,2013

UniProt 2013_10, PDB 2013-10-12 was released.

Services: ddbj Keywords: Data Release

PDB 2013-10-19 released

October 19,2013

PDB 2013-10-19 was released.

Services: ddbj Keywords: Data Release

Release of cDNA sequence data of Brachypodium distachyon

October 15,2013

DDBJ released cDNA sequence data of Brachypodium distachyon, which had been submitted by RIKEN.

Reference
RIKEN Brachypodium FLcDNA database
The accession numbers are as follows. They are available on getentry.

    5'-EST: HX789325-HX828682 (39,358 entries)
    3'-EST: HX828683-HX867487 (39,247 entries)
    HTC: AK424275-AK440353 (16,079 entries)
Services: ddbj Keywords: Data Release

(Oct. 19) NIG and DDBJ network temporary down

October 11,2013

NIG (National Institute of Genetics) and DDBJ network will be unavailable at the following schedule because of the network maintenance.

  • Date: Oct. 19(Sat), 2013 at 14:00 - 16:00 (JST)
            (60 minutes interception during this time)

Thank you for your cooperation.
Services: ddbj Keywords: Maintenance

PDB 2013-10-05 released.

October 10,2013

PDB 2013-10-05 was released.

Services: ddbj Keywords: Data Release

UniProt 2013_09 released

September 26,2013

UniProt 2013_09 was released.

Services: ddbj Keywords: Data Release

System temporarily unavailable

September 20,2013
From 9:00 to 15:00, 25th (Wed) Sep., DRA and BioProject submission and search services will be unavailable due to system maintenance.
Services: bioproject,biosample,gea,dra,dta,jga Keywords: Maintenance

DDBJ Rel. 94.0, DAD Rel. 64.0 Completed

September 18,2013

DDBJ Rel. 94.0

DAD (DDBJ amino acid database) Rel. 64.0
  • Date: Sep. 18, 2013
  • 28,416,672 entries     8,394,552,710 aa (total number of residues)
  • DAD Release Note
Services: ddbj Keywords: Data Release

Please change settings for news RSS

September 17,2013

The RSS distribution URL of DDBJ news will be changed. Please change your RSS registration URL. Details are as follows:

  • Date of change:From Sep. 17(Tue), 2013
  • New URL:
    http://www.ddbj.nig.ac.jp/feed?post_type=news-e(English)
    http://www.ddbj.nig.ac.jp/feed?post_type=news-j(Japanese)
Thank you for your understanding and cooperation.
Services: ddbj Keywords: Announcement

Aplogy for the DDBJ service down due to the lightgning strikes of Aug. 21

August 28,2013
Due to the emergency shutdown of NIG supercomputer system caused by the lightning strikes to the Mishima area (DDBJ locates) at 19:00(JST) of Aug.21 , most of DDBJ services had been unavailable until Aug.23.DDBJ sincerely apologizes for your inconveniences because of the long-time suspension of many services.
Services: ddbj Keywords: Maintenance

System temporarily unavailable

August 27,2013
From 9:30 to 10:30, 28th (Wed) Aug., DRA and BioProject submission and search services will be unavailable due to system maintenance.
Services: bioproject,biosample,gea,dra,dta,jga Keywords: Maintenance

12-13, August: Suspension of some parts of DDBJ activities during summer holidays

August 09,2013
DDBJ will suspend our business on releasing data and answering inquiries from 12 to 13, August, 2013 (JST) due to summer holidays of our institute. We will reply to your messages on or after August 14. All web services are available. Thank you for your understanding and cooperation.
Services: bioproject,biosample,gea,dra,dta,jga Keywords: Announcement

The Report for the 26th International Collaborators Meeting

August 09,2013
International Nucleotide Sequence Database Collaboration (INSDC), consisted of DDBJ, EBI and NCBI, hold the international collaborators meeting every year.
In 2013, the meeting was held at EBI in UK, 21-23 May, to discuss practical matters to maintain and update nucleotide sequence data archives; DDBJ, EMBL-Bank, GenBank, Sequence Read Archive (SRA) and Trace Archive.
The outcomes of the meeting are summarized here.
Services: ddbj Keywords: Announcement

(Aug. 15) NIG and DDBJ network temporary down

August 07,2013

NIG (National Institute of Genetics) and DDBJ network will be unavailable at the following schedule because of the network maintenance.

  • Date: Aug. 15(Thu), 2013 at AM 0:00 - 6:15 (JST)
            (10 minutes interception during this time)

Thank you for your cooperation.
Services: ddbj Keywords: Maintenance

Apologies for defects in TPA data from EMBL-Bank

August 06,2013

Some disorders were found in the process of sorting TPA data from EMBL-Bank.
Details are as follows:

Coverage: Subset of TPA data from EMBL-Bank, 865 entries with following accession numbers.
  HE804769-HE804772  HG322958-HG323812  BN001513-BN001519  FR749997
Period: From 2013.04.24 to 2013.07.27
Services: anonymous FTP,getentry
Situation:In anonymous FTP: Intrinsically, TPA data should be separated into a directory (/ddbj_database/tpa/ddbjnew/) to distinguish from primary data. However, following TPA entries were included in the same files with primary data.
directory: ftp://ftp.ddbj.nig.ac.jp/ddbj_database/ddbjnew/file name: 
DDBJNEWr93.043.dat.gz (contains HG322958-HG323812)           
DDBJNEWr93.046.dat.gz (contains HG322958-HG323812)           
DDBJNEWr93.050.dat.gz (contains BN001513-BN001519,FR749997)          
 DDBJNEWr93.054.dat.gz (contains HG322958-HG323812)           
DDBJNEWr93.056.dat.gz (contains HG322958-HG323812)           
DDBJNEWr93.065.dat.gz (contains HG322958-HG323812)
In getentry: The TPA entries were not loaded into getentry.

Measure: We have fixed the relevant software tool.
For anonymous FTP: The TPA entries will be reallocated correctly after DDBJ periodical release 94.
For getentry: The TPA entries have been loaded into getentry.

We apologize for your inconvenience.

Services: ddbj Keywords: Announcement

Release of genome sequence data of a coral symbiont, Symbiodinium minutum

August 02,2013

DDBJ released genome sequence data of a coral symbiont, Symbiodinium minutum, which had been submitted by Okinawa Institute of Science and Technology.

Reference; A coral symbiont genome decoded for first time
The accession numbers are as follows. They are available on getentry and DRASearch.

    scaffold CON: DF239013-DF260911 (21,899 entries)
    WGS: BASF01000001-BASF01033816 (BASF.gz) (33,816 entries)
    raw data: DRR003834-DRR003864

    GSS: GA393224-GA605429 (212,206 entries)

Services: ddbj Keywords: Data Release

24th, July (Wed) 9:30-10:30 system maintenance

July 19,2013
DRA submission, search and ftp download services at ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/ERX/ will be unavailable.
Services: bioproject,biosample,gea,dra,dta,jga Keywords: Maintenance

Update of TPA CON data of vase tunicate (Ciona intestinalis)

July 17,2013

DDBJ updated TPA CON data of vase tunicate (Ciona intestinalis), which had been submitted by Kyoto University.
The accession numbers are as follows. They are available on getentry.
    TPA CON: HT000001-HT001272 (1,272 entries)

Services: ddbj Keywords: Announcement

(Aug.12-13)Suspension of some parts of DDBJ activities during summer holidays

July 13,2013
DDBJ will suspend our business on releasing data and answering inquiries from August 12 to 13, 2013(JST) due to NIG summer holidays. We will reply to your messages on or after August 14. But, all WWW services are available.

Thank you for your understanding and cooperation.
Services: ddbj Keywords: Maintenance

Website renewal with new DDBJ logo

July 09,2013
Our website was renewed with new DDBJ logo.
Services: bioproject,biosample,gea,dra,dta Keywords:

Release of genome sequence data of Pacific bluefin tuna (Thunnus orientalis)

July 09,2013

DDBJ released genome sequence data of Pacific bluefin tuna (Thunnus orientalis), which had been submitted by National Research Institute of Fisheries Science.
The accession numbers are as follows. They are available on getentry.
    WGS: BADN01000001-BADN01133062 (BADN.gz) (133,062 entries)

Services: ddbj Keywords: Announcement

DDBJ Rel. 93.0, DAD Rel. 63.0 Completed

June 11,2013
DDBJ Rel. 93.0
DAD (DDBJ amino acid database) Rel. 63.0
  • Date: Jun. 11, 2013
  • 27,454,545 entries     8,076,539,495 aa (total number of residues)
  • DAD Release Note
Services: ddbj Keywords: Announcement

(Jun 6, 17:30-) All DDBJ web services unavailable for supercomputer maintenance(Resumed)

June 06,2013
Due to emrgency maintenance works of NIG super computer system, DDBJ network services will be unavailable around 17:30 (JST) of today (June 6, 2013). Detailed suspension schedule will be announced on this DDBJ HP soon.
Scheduled (JST)Services
Jun. 6 (Thu), 17:30 (JST) - Jun. 07 (Fri), 10:00(Resumed)DDBJ HP
Jun. 6 (Thu), 17:30 (JST) - Jun. 07 (Fri), 12:00
(Resumed)
· getentry
· ARSA
· D-way
· DRA Search
· BioProject Search
· BLAST
· ClustalW
· DDBJ Nucleotide Sequence Submission System
DDBJ apology for your inconvenience.Thank you for your cooperation and understanding.
June 6, 2013 at 17:45(JST)
Services: ddbj Keywords: Maintenance

(Jun 6) DDBJ services unavailable for emrgency maintenance of super computer

June 06,2013
Due to emrgency maintenance works of NIG super computer system, DDBJ network services will be unavailable from 19:00 (JST) of today (June 6, 2013). Detailed suspension schedule will be announced on this DDBJ HP soon.DDBJ apology for your inconvenience.Thank you for your cooperation and understanding.
June 6, 2013
Services: ddbj Keywords: Maintenance

(Jun. 14) NIG and DDBJ network temporary down

May 30,2013

NIG (National Institute of Genetics) and DDBJ network will be unavailable at the following schedule because of the network maintenance.

  • Date: Jun. 14(Fri), 2013 at AM 0:00 - 2:00 (JST)
            (60 minutes interception during this time)
Thank you for your cooperation.
Services: ddbj Keywords: Maintenance

Notice for an emergency maintenance

May 27,2013

For an emergency maintenance, D-way, DRA and BioProject systems are not available. For details, please see DDBJ homepage.

Services: bioproject,biosample,gea,dra,dta,jga Keywords: Maintenance

Services reopened

May 21,2013

D-way submission, DRA and BioProject search systems are reopened.

Services: bioproject,biosample,gea,dra,dta Keywords: Maintenance

Service reopen time extended

May 20,2013

Reopen of currently suspended D-way submission, DRA and BioProject search systems are extended. We are planning to reopen services tomorrow (21th, May).

Services: dra,dta Keywords: Maintenance

(May 17-20) Some functions of DDBJ services are unavailable(all service resumed)

May 13,2013
Some functions of DDBJ services will be unavailable at the following schedule because of the NIG(National Institute of Genetics) network system maintenance.

All Services and functions are resumed. DDBJ apologizes for your inconvenience. (May 21 11:50(JST)).

ServicesUnavailable functionsPeriod
DDBJ Home PageSubmission of inquiries
Mass Submission System application
May 17 (Fri) 18:00 (JST) -
May 18 (Sat) 09:00 (JST)
DDBJ Sequence Read Archive
DDBJ Trace Archive
DDBJ BioProject
Creating D-way submission account
Data Submission·Update (via D-way)
Data Search
May 17 (Fri) 15:00 (JST) -
getentry
ARSA
Data release
Data update
May 17 (Fri) 15:00 (JST) -
May 20 (Mon) 12:00 (JST)
deferred data will be released/updatted after the service resumption
FTPData download
Data release·update
May 18 (Sat) 15:00 (JST) -
Thank you for your cooperation and understanding.

May 13, 2013
Services: ddbj Keywords: Maintenance

Services temporarily unavailable

May 10,2013
From 15:00, 17th (Fri), May to noon, 21th (Tue), D-way submission, DRA and BioProject search services will be unavailable due to system switching.
Services: bioproject,biosample,gea,dra,dta Keywords: Maintenance

Website renewal

April 25,2013
Services: bioproject,biosample,gea,dra,dta Keywords:

Suspension of some parts of DDBJ activities during Japanese holidays

April 22,2013
We at DDBJ will suspend our business on releasing data and answering inquiries from April 27 to 29 and from May 3 to 6, 2013. Search, analysis and other WWW services are available. We will resume the normal business from May 7.
Thank you for your understanding and cooperation.
Services: ddbj Keywords: Announcement

Release of genome sequence data of mouse (Mus musculus strain MSM/Ms)

April 19,2013

DDBJ released genome sequence data of mouse (Mus musculus strain MSM/Ms), which had been submitted by National Institute of Genetics.
The accession numbers are as follows. They are available on getentry.
    WGS: BAAG010000001-BAAG011237600 (BAAG.gz) (1,237,600 entries)

Services: ddbj Keywords: Announcement

Release of genome sequence data of a biofuel crop, Jatropha curcas

April 15,2013

DDBJ released genome sequence data of a biofuel crop, Jatropha curcas, which had been submitted by the Kazusa DNA Research Institute.
The sequence data are updated version of previously released one.
Reference URL;
    Jatoropha database
The accession numbers are as follows. They are available on getentry and DRASearch.
    scaffold CON: DF145383-DF157092 (11,710 entries)    WGS: BABX02000001-BABX02066610 (BABX.gz) (66,610 entries)    raw data: DRR001794, DRR001795

Services: ddbj Keywords: Announcement

DDBJ services temporary unstable due to network failure

April 04,2013

Because of the network system failure, some DDBJ services are temporary unstable connection.
Recovery works are in operation. We will announce on this page as soon as the maintenance are completed.
Thank you very much for your understanding and cooperation.


System failure was resolved, and DDBJ services operates normally.We apologize for you inconvenience. (at 9:00 Apr. 5, 2013(JST))

Services: ddbj Keywords: Maintenance

Enhancement in DDBJ BLAST

April 02,2013
DDBJ greatly improved the homology search BLAST.
  • Selections of Data Sets and Divisions were modified
  • Get the result by E-mail, as well as in the web screen
  • Direct link to the flat file of the corresponding accession number
  • Link-up to ClustalW
  • Request ID was not included in the URL of the result
  • New function Result Viewer was equipped

Selections of Data Sets and Divisions were modifi

(1) Datasets are selected from DDBJ ALL, DDBJ New, 16SrRNA (in case of nucleotide)
(2) In the specification of Divisions, you can select general classifications (Standard divisions, High thryoughput divisions, EST divisions , Other divisions), and detailed specification of divisions are available.

 

get the result by E-mail, as well as web screen

You can select the method of getting the result either E-mail or WWW. 

direct link to the flat file of the corresponding accession number

You can view the flatfile of the sequences in the getentry. 

Request ID was not included in the URL of the result

After pressing the "Send to BLAST" button, Request ID is displayed on the web screen. Don't loose this ID because it is necessary for using the "Result Viewer" and/or inquiring to DDBJ for your search. 

New function Result Viewer

You can view your result using "Request ID" at any time (within the retention period). 

Link-up to ClustalW

Select the sequences which you would like to suceed the clustalW, then press the "ClustalW" button. Your selected sequences are automatically pasted in the ClustalW query box. 

DDBJ will continue to improve the services. Your revies and comments will be helpful for DDBJ's improvement. Please send your comments from "Contact Us" page. (Please select the item "Web Support ")
Services: ddbj Keywords: Announcement

Release of EST data of white-tufted-ear marmoset (Callithrix jacchus)

April 02,2013

DDBJ released 5'-EST data derived from white-tufted-ear marmoset (Callithrix jacchus), which had been submitted by National Institute of Genetics.

The accession numbers are as follows. (Available by getentry)

    EST: HX373156-HX663542 (290,387 entries)

Services: ddbj Keywords: Announcement

DDBJ Rel. 92.0, DAD (DDBJ amino acid database) Rel. 62.0 Completed

March 21,2013
DDBJ Rel. 92.0
DAD (DDBJ amino acid database) Rel. 62.0
  • Date: Mar. 21, 2013
  • 26,351,045 entries     7,698,263,093 aa (total number of residues)
  • DAD Release Note
Services: ddbj Keywords: Announcement

Release of TSA data of forest soil metagenome

March 18,2013

DDBJ released TSA data derived from forest soil metagenome, which had been submitted by National Institute of Advanced Industrial Science and Technology.

The accession numbers are as follows. (Available by getentry and DRASearch)

    TSA: FX000001-FX056084 (56,084 entries)
    raw data: DRR000345

Services: ddbj Keywords: Announcement

Changes in the anonymous FTP site: Added a new directory "unified-all" and rename from "non-redundant" to "unified-new"

March 07,2013

A new directory "unified-all" was added under "ddbj_database" of DDBJ anonymous FTP site. With this addition, a directory, "non-redundant", was renamed to "unified-new"
About the "ddbj_database" directory and its sub-directories, please refer to the README.TXT in the directory. When you monitor the FTP site, please confirm your monitoring program, if necessary.

unified-all; ftp://ftp.ddbj.nig.ac.jp/ddbj_database/ddbjnew/unified-all
This directory contains files of merged sequence entries from all files of ddbj and ddbjnew directories to include only latest version of updated entries (i.e. Succeeded versions of entries have been excluded).
Contents of the directory unified-all  |- fasta   : in FASTA file format  
|- blastdb : in BLAST DB format
unified-new; ftp://ftp.ddbj.nig.ac.jp/ddbj_database/ddbjnew/unified-new
This directory contains files of merged cumulative daily updates of sequence entries from all files of ddbjnew directory to include only latest version of updated entries (i.e. Succeeded versions of entries have been excluded) in the flat file format.
Contents of the directory unified-new  : in DDBJ flat file format  |- fasta   : in FASTA file format  
|- blastdb : in BLAST DB format
Services: ddbj Keywords: Announcement

(Mar.8-11)DDBJ network services will be unavailable for power outage

February 28,2013
DDBJ network services will be unavailable at the following schedule because of the electric power outage of the NIG(National Institute of Genetics) and maintenance of the NIG SuperComputer.
Please note that the suspended period depends on the service.

ServicesScheduled (JST)
getentry, ARSA, Anonymous-FTP
D-way, DRA, DTA, BioProject,
Mar. 8 (Fri), 13:00 - Mar. 11 (Mon), 12:00
DDBJ HP, NIG SuperComputer,
DDBJ Nucleotide Sequence Submission System,
BLAST, ClustalW,
DDBJ Read Annotation Pipeline, MiGAP,
Mar. 8 (Fri), 17:00 - Mar. 11 (Mon), 9:00
*an optional extra day: Mar. 11 (Mon), 24:00
Thank you for your cooperation and understanding.

February 28, 2013
Services: ddbj Keywords: Maintenance

Apologies for defects in WGS data from EMBL-Bank

February 13,2013

Some disorders were found in a software tool to load WGS data from EMBL-Bank.
Details are as follows:

Coverage: Subset of WGS data from EMBL-Bank, 64,579 entries with following 175 prefixes.
See also the list of publicized WGS data.
CABT, CACQ, CADR, CAEG, CAEK, CAEL, CAEN, CAEO, CAEP, CAER, CAES, CAET, CAEU, CAEV, 
CAEW, CAFD, CAFH, CAFI, CAFJ, CAFK, CAFM, CAFN, CAFQ, CAGA, CAGB, CAGD, CAGH, CAGI, 
CAGJ, CAGK, CAGL, CAGM, CAGN, CAGO, CAGP, CAGQ, CAGR, CAGS, CAGT, CAGU, CAGV, CAGW, 
CAGX, CAGY, CAGZ, CAHA, CAHB, CAHC, CAHD, CAHE, CAHF, CAHG, CAHH, CAHI, CAHJ, CAHK, 
CAHL, CAHN, CAHO, CAHP, CAHR, CAHT, CAHU, CAHV, CAHW, CAHX, CAHZ, CAIA, CAIB, CAIE, 
CAIF, CAIG, CAIH, CAII, CAIJ, CAIK, CAIL, CAIM, CAIN, CAIO, CAIP, CAIQ, CAIR, CAIT, 
CAIU, CAJD, CAJE, CAJF, CAJH, CAJJ, CAJK, CAJL, CAJM, CAJN, CAJO, CAJP, CAJQ, CAJR, 
CAJS, CAJT, CAJU, CAJY, CAJZ, CAKA, CAKB, CAKC, CAKD, CAKE, CAKF, CAKM, CAKN, CAKO, 
CAKP, CAKQ, CAKR, CAKS, CAKT, CAKU, CAKV, CAKW, CAKX, CAKY, CAKZ, CALA, CALB, CALC, 
CALD, CALE, CALF, CALG, CALI, CALJ, CALK, CALL, CALU, CALV, CALW, CALX, CALY, CALZ, 
CAMA, CANE, CANF, CANG, CANH, CANI, CANJ, CANO, CANP, CANQ, CANR, CANS, CAOH, CAOI, 
CAOL, CAOM, CAON, CAOO, CAOR, CAOS, CAOT, CAOU, CAOV, CAPF, CAPG, CAPH, CAPI, CAPJ, 
CAPK, CAPL, CAPM, CAPN, CAPS, CAQO, CAQP
Period: From 2012.03.01 to 2013.02.12
Situation: Invalid format of division in LOCUS line
Services: Anonymous FTP,getentry
Measure: We redistributed and applied the data after fixing the software.

We apologize for your inconvenience.

Services: ddbj Keywords: Announcement

BioSample does not accept submissions.

January 30,2013
At present, DDBJ BioSample does not accept any submissions. The DDBJ will announce the launch of BioSample when it is ready.
Services: biosample Keywords:

DAD Rel. 61.1 released

January 22,2013
DAD Rel.61.1 was released, because some disorders were found in DAD Rel.61.0 (released on December 2012).

    Services: ddbj Keywords: Announcement

    Apologies for defects in DAD data

    January 18,2013

    Some disorders were found in a software tool to generate DAD entries from DDBJ entries.
    Details are as follows:

    Category 1
    Coverage: Subset of DAD entries, DAD release notes
    Period: From 2011.11.26 (DAD entries generated after DAD Rel. 58)
    Situation: Invalid format of LOCUS line, Statistics in DAD release notes were not correct.

    Category 2
    Coverage: Subset of DAD entries
    Period: Not clear
    Situation: Invalid format of DEFINITION line, COMMENT line and part of features
    For both categories 1 and 2
    Services: Anonymous FTP,getentry
    Measure: We will redistribute and apply DAD release 61.1 after fixing the software.

    Please note DAD fasta files are generated in a normal way, independently of those disorders.

    We apologize for your inconvenience.

    Services: ddbj Keywords: Announcement

    Release of GSS data of African clawed frog (Xenopus laevis)

    January 17,2013
    DDBJ newly released GSS data derived from African clawed frog (Xenopus laevis), which had been submitted by National Institute of Genetics.

    Available at getentry.
    The accession numbers are as follows;

    • GSS: GA720358-GA867435 (147,078 entries)
    Services: ddbj Keywords: Announcement
    • Partners

    • NIG logo
    • ROIS logo
    • JBI logo
    • NBDC logo
    • DBCLS logo
    • PDBj logo