DDBJ Center News Archive

News from 2011

Release of genome sequence data of Hitomebore rice (Oryza sativa Japonica Group cv. Hitomebore)

2011年12月28日
DDBJ newly released WGS and scaffold CON data derived from Hitomebore rice (Oryza sativa Japonica Group cv. Hitomebore), which had been submitted by Iwate Biotechnology Research Center.  (Available by getentry )

The accession numbers are as follows ;
  • WGS                BACJ01000001 - BACJ01064745 (BACJ.gz) ( 64,745 entries)
  • scaffold CON     DG000053 - DG000064 ( 12 entries)
Services: ddbj Keywords: Announcement

DDBJ/EMBL/GenBank Feature Table Definition revised

December 22,2011
Feature Table Definition (FT-Doc) 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. Feature Table Definition was revised in December 2011. Version is 10.0.
Services: ddbj Keywords: Announcement

(All services were resumed) (2012/1/12-18) DDBJ network services temporary down

December 21,2011
All DDBJ network service will be unavailable, because of the preliminary works for the computer system replacement in NIG scheduled in March, 2012.Details are as follows:
[generate_table class=t02]ServicesScheduled (JST)SAKURAJan. 12 (Thu), 2012 17:00 - Jan. 18 (Wed) 10:00 DDBJ HPJan. 13 (Fri), 2012 15:00 - Jan. 16 (Mon) 14:00 OtherJan. 13 (Fri), 2012 15:00 - Jan. 16 (Mon) 16:00[/generate_table]
Thank you for your cooperation and understanding.
All services were resumed. Thank you for your cooperation. (Jan. 18 at AM 10:00 JST)
Services: ddbj Keywords: Maintenance

Release of MGA data of human (Homo sapiens)

December 06,2011
DDBJ newly released 5'SAGE tags, MGA data, derived from human (Homo sapiens), which had been submitted by University of Tokyo.The accession numbers are as follows;
AEAAA0000001-AEAAA0026367 (26,367 entries)AEAAB0000001-AEAAB0012114 (12,114 entries)
AEAAC0000001-AEAAC0021096 (21,096 entries)AEAAD0000001-AEAAD0024262 (24,262 entries)
AEAAE0000001-AEAAE0023437 (23,437 entries)AEAAF0000001-AEAAF0030485 (30,485 entries)
AEAAG0000001-AEAAG0021798 (21,798 entries)AEAAH0000001-AEAAH0040734 (40,734 entries)
AEAAI0000001-AEAAI0029614 (29,614 entries)AEAAJ0000001-AEAAJ0030206 (30,206 entries)
Anonymous FTP: AE_resource_indexRelated site: About Mass sequence Genome for Sequence (MGA) entry
Services: ddbj Keywords: Announcement

Suspension of the DDBJ activity during the New Year Holidays

November 29,2011
We at DDBJ will temporally close our business for the New Year Holidays in the following schedules, according to the Japanese custom, and resume the normal business on January 4, 2012.
Please note in particular that SAKURA will also stop in operation for a while (see below). However, the computer search and analysis and FTP are available during the holidays.

DDBJ activity suspension:Dec. 29(Thu), 2011 - Jan. 3(Tue), 2012    
SAKURA suspension:Dec. 27(Tue), 2011 at 17:00(JST) - Jan. 4(Wed), 2012 at 10:00(JST)
data release suspension:Dec. 27(Tue), 2011 - Jan. 4(Wed), 2012
Thank you for your understanding and cooperation.

November 29, 2011     DDBJ
Services: ddbj Keywords: Maintenance

(Dec. 6) NIG and DDBJ network temporary down

November 16,2011
NIG (National Institute of Genetics) and DDBJ network will be unavailable at the following schedule because of the network maintenance.

  • Date: Dec. 6 (Tue), 2011 at 18:30 - 19:30 (JST) (15 minutes interception during this time)
Thank you for your cooperation.
Services: ddbj Keywords: Maintenance

D-way, DRA submission system and manuals are updated.

October 25,2011
D-way Submission Account Manual
"DRA/BioProject Submission Manual"
In the D-way website, please reference the list of registered projects at the "Project List" menu and submit a new project from the "BioProject" menu.
Services: dra Keywords:

(11/11-14) DDBJ network services are unavailable for power outage of the NIG

October 25,2011
DDBJ network services will be unavailable at the following schedule because of the electric power outage of the NIG(National Institute of Genetics). Please note that the suspended period depends on the service.
ServicesScheduled (JST)
DDBJ Read Annotation PipelineNov. 11 (Fri) 12:00 - Nov. 14 (Mon) 12:00
SAKURANov. 11 (Fri) 13:00 - Nov. 14 (Mon) 12:00
D-way, DRA, DTA, BioProject, CIBEX,
getentry, ARSA,
BLAST, ClustalW,
TXSearch, Vector Screening System,
GIB, Anonymous-FTP, WABI
Nov. 11 (Fri) 15:00 - Nov. 14 (Mon) 12:00
DDBJ HPNov. 11 (Fri) 17:00 - Nov. 12 (Sat) 18:00
Thank you for your cooperation and understanding.
All services were resumed. Thank you for your cooperation. (Nov. 14 at 12:00 JST)
Services: ddbj Keywords: Maintenance

(Dec. 6)NIG and DDBJ network temporary down

October 25,2011
NIG (National Institute of Genetics) and DDBJ network will be unavailable at the following schedule because of the network maintenance.

  • Date: Dec. 6(Tue), 2011 at 18:30 - 19:30 (JST) (15 minutes interception during this time)
Thank you for your cooperation.
Services: ddbj Keywords: Maintenance

DDBJ starts BioProject services

October 25,2011
The BioProject database represents a higher order organization of research projects and the corresponding data which is deposited into several archival databases maintained by members of INSDC. Data submitted to INSDC-associated databases cross-reference the BioProject identifier to support navigation between the project and the project's datasets.The DDBJ BioProject issues internationally-recognized accession numbers with the prefix 'PRJD' to the submitted projects. Public project data are exchanged with the EBI and NCBI.

You need to obtain an account of DDBJ submission portal ‘D-way’ to submit your project data. Please obtain an account according to the submission account manual and submit your project data from the D-way website.

D-way Submission Account Manual (Japanese)
D-way Submission Account Manual (English)

If you have questions, please contact us.
Services: ddbj Keywords: Announcement

Release of WGS and scaffold CON data of a liver fluke (Clonorchis sinensis)

October 24,2011
DDBJ newly released WGS and scaffold CON data derived from a liver fluke (Clonorchis sinensis), which had been submitted by Sun Yat-sen University (China).  (Available by getentry )

The accession numbers are as follows ;
  • WGS                BADR02000001 - BADR02006190 (BADR.gz) ( 6,190 entries)
  • scaffold CON     DF142828 - DF145382 ( 2,555 entries)
Services: ddbj Keywords: Announcement

DDBJ BioProject is launched.

October 24,2011
DDBJ BioProject is launched.
Services: bioproject Keywords:

Resumed GIB

October 03,2011
GIB has been resumed since October 3, 2011.
For electricity conservation, we stopped and kept you waiting for a long time.
Please use it.
Services: ddbj Keywords: Announcement

(Sep. 30) ARSA database search temporary unavailable

September 26,2011
ARSA is a high-speed data retrieval system provided by DDBJ via WWW and Web API. DDBJ and DAD database search in ARSA is unavailable in the following schedule to update each of released data (DDBJ Release 87.0 and DAD Release 57.0).

Details are as follows:
  • Date & Time:
      Sep. 30, 2011 (Fri) 9:00 - 20:00 JST (We will announce on this page when the service resumes)
  • Unavailable related services:
      ARSA reference function in TX Search
      DNA/Protein/AllDBs search at the search box of the upper part of DDBJ HP
Thank you for your understanding and cooperation.
Maintenance works finished. Thank you for your cooperation. (Sep. 30, 2011 at 18:40)
Services: ddbj Keywords: Maintenance

DDBJ Rel. 87.0, DAD (DDBJ amino acid database) Rel. 57.0 Completed

September 26,2011
DDBJ Rel. 87.0DAD (DDBJ amino acid database) Rel. 57.0
Services: ddbj Keywords: Announcement

Release of WGS and scaffold CON data of a liver fluke (Clonorchis sinensis)

September 26,2011
DDBJ newly released WGS and scaffold CON data derived from a liver fluke (Clonorchis sinensis), which had been submitted by Sun Yat-sen University (China).

The accession numbers are as follows ;
  • WGS                BADR01000001 - BADR01060778 (BADR.gz) ( 60,778 entries)
  • scaffold CON     DF126616 - DF142827 ( 16,212 entries)  (Available by getentry )
Services: ddbj Keywords: Announcement

The Report for the 24th International Collaborators Meeting

September 22,2011
International Nucleotide Sequence Database Collaboration (INSDC), consisted of DDBJ, EBI and NCBI, hold the international collaborators meeting every year.In 2011, the meeting was held at Osaka in Japan, 23-27 May, to discuss practical matters to maintain and update nucleotide sequence data archives; DDBJ, EMBL-Bank, GenBank, Sequence Read Archive (SRA) and Trace Archive.Though there were still aftermaths of the Great East Japan Earthquake, DDBJ could host ICM2011 with understanding and cooperation of NCBI and EBI.The outcomes of the meeting are summarized here.
Services: ddbj Keywords: Announcement

Release of EST and full length cDNA sequence data of silkworm (Bombyx mori)

September 16,2011
DDBJ newly released EST and full length cDNA sequence data derived from silkworm (Bombyx mori), which had been submitted by National Institute of Agrobiological Sciences.  (Available by getentry)
Reference: Silkworm Genome Research Program (SGP)The accession numbers are as follows;[EST]FS724152 - FS939542 ( 215,391 entries)FY736910 - FY762881 ( 25,972 entries)[full length cDNA (including HTC)]AK377185 - AK388575 ( 11,160 entries; 231 entries dropped)
in detailsAK377185 - AK377195AK377197 - AK388061AK388063 - AK388065AK388068 - AK388069AK388077 - AK388079AK388100 - AK388102AK388104AK388121AK388124AK388126AK388128AK388131AK388145 AK388148AK388150AK388157AK388182AK388184 - AK388185AK388197AK388200AK388215AK388222AK388230AK388241AK388244 - AK388245AK388247AK388249AK388255AK388258 - AK388260AK388263 - AK388264AK388267AK388275 - AK388276AK388283AK388287 - AK388288AK388297 AK388310 - AK388311AK388318 - AK388322AK388327 - AK388328AK388330AK388341 - AK388369 AK388371 - AK388381AK388383 - AK388391AK388394 - AK388395AK388397 - AK388428 AK388430 - AK388473AK388475 - AK388499AK388501 - AK388575
Services: ddbj Keywords: Announcement

Release of WGS and scaffold CON data of sake yeast (Saccharomyces cerevisiae Kyokai no. 7)

September 13,2011
DDBJ newly released WGS and scaffold CON data derived from sake yeast (Saccharomyces cerevisiae Kyokai no. 7), which had been submitted by National Research Institute of Brewing.  (Available by getentryReference: Sake yeast genome database (SYGD)The accession numbers are as follows;
  • WGS    BABQ01000001 - BABQ01000705 (BABQ.gz) ( 705 entries)
  • scaffold CON    DG000037 - DG000052 ( 14 entries)
  • mitochondrion    AP012028
Services: ddbj Keywords: Announcement

ARSA DDBJ database search temporary unavailable

September 12,2011
ARSA is a high-speed data retrieval system provided by DDBJ via WWW and Web API. DDBJ database search in ARSA is unavailable due to the system error. Details are as follows:
  • Date & Time: Sep. 12, 2011 (Mon) AM 8:08 (JST) -- (We will announce on this page when it resumes.)
  • Suspended services: DDBJ in ARSA
  • Note: Searchable DB is DAD only
Thank you for your understanding and cooperation.
Maintenance works finished. Thank you for your cooperation. (Sep. 12, 2011 at 19:00 JST)
Services: ddbj Keywords: Maintenance

The SRA xml schema 1.3 has been installed

September 11,2011
The SRA xml schema 1.3 has been installed. Please see full release notes.
Services: dra Keywords:

Change in the anonymous FTP site: Added a new directory "bioproject"

September 01,2011
A new directory "bioproject" was added under "ddbj_database" of DDBJ anonymous FTP site. All of released data from DDBJ BioProject will be available at the new "bioproject" directory.About the "ddbj_database" directory and its sub-directories, please refer to the README.TXT in the directory. If you monitor the DDBJ anonymous FTP, please confirm your monitoring program if necessary.
Services: ddbj Keywords: Announcement

DDBJ BioProject website open

August 31,2011
The BioProject database represents a higher order organization of research projects and the corresponding data which is deposited into several archival databases maintained by members of the INSDC.Data submitted to INSDC-associated databases cross-reference the BioProject identifier to support navigation between the project and the project’s datasets. At the DDBJ, records in the following DDBJ archival databases are grouped: DDBJ nucleotide sequence database, Sequence Read Archive and Trace Archive.The BioProject record has information about a project's scope, material, objectives, funding source and general relevance categories.The BioProject resource is a redesigned, expanded, replacement of the NCBI Genome Project resource.The DDBJ BioProject issues internationally-recognized accession numbers with the prefix 'PRJD' to the submitted projects.Public project data are exchanged with the EBI and NCBI. * The BioProject resource is released in phases. After the release of interactive submission system, we will start to accept new BioProject submissions.
Services: ddbj Keywords: Announcement

(Sep.4 & 5)NIG and DDBJ network temporary down

August 23,2011
NIG (National Institute of Genetics) and DDBJ network will be unavailable at the following schedule because of the network maintenance.

  • Date: Sep. 4(Sun), 2011 at AM 2:30 - AM 3:30 (JST)
             Sep. 5(Mon), 2011 at AM 1:00 - AM 3:00 (JST) (60 minutes interception during this time)
Thank you for your cooperation.
Services: ddbj Keywords: Maintenance

Directory and file names for quality scores will be changed

August 17,2011
DDBJ will change directory and file names for quality scores of anonynmous FTP, on 23 August 2011.

FTP server   ftp://ftp.ddbj.nig.ac.jp/

directory name ;from /ddbj_database/ddbjnew/qvalue/to   /ddbj_database/ddbjnew/qscore/

file name ;from DDBJNEWr##.###.qvalue.gzto   DDBJNEWr##.###.qscore.gz

For details, please see README.TXT after 23 August.If you automatically monitor DDBJ anonymous FTP, please confirm your monitoring program if necessary.
Services: ddbj Keywords: Announcement

The fax number changed to "Mandatory"

August 17,2011
SAKURA is a nucleotide sequence data submission system through the WWW server at DDBJ.The input of the fax number changed to "Mandatory(Marked with )" on 15 August 2011. You can't proceed further if you fail to fill up any one of the fields.Generally, DDBJ contacts submitters via E-mail. However, in case of breakdown of communication via E-mail by any reason, DDBJ would contact submitters via fax.So, please let us know your fax number, if possible.Please choose "If you do not have any fax machine, please check it." if you do not have the fax.Thank you for your understanding and cooperation.
Services: ddbj Keywords: Announcement

Release of new EST data of sea squirt (Halocynthia roretzi)

August 03,2011
DDBJ newly released EST data derived from sea squirt (Halocynthia roretzi), which had been submitted by University of Tokushima.

Reference: MAGEST

The accession numbers are as follows ;
  • FY844421-FY896670 (52,250 entries)    (Available by getentry)
Services: ddbj Keywords: Announcement

DDBJ HP renewal

August 01,2011
DDBJ  renewed HP in August 1, 2011, and changed the following points.RSS of "Update information" in the top page was shifted to getentry.In the top page, a new RSS for the latest news such as "Hot Topics"starts. So, please change settings.The twitter icon is  set up in top page. "Follow", please. Google Search is applied to the "Site Search".Thank you for your understanding and cooperation.
Services: ddbj Keywords: Announcement

Release of new WGS data of Acropora digitifera

July 29,2011
DDBJ newly released WGS and scaffold CON data derived from Acropora digitifera, which had been submitted by Okinawa Institute of Science and Technology.

Reference:

The accession numbers are as follows ;
  • WGS                BACK01000001-BACK01053640 (BACK.gz) (53,640 entries)
  • scaffold CON     DF093604-DF097774 (4,171 entries)  (Available by getentry )
Services: ddbj Keywords: Announcement

Please change settings of RSS

July 28,2011
DDBJ HP will be renewed in August 1, 2011, and RSS is also changed as follows:RSS of "Update Information" (of the data release) which is currently placed in the top page is shift to getentry. Please change settings of this RSS.In the top page, a new RSS for the latest news such as "Hot Topics" starts. You can set it after renewal.Thank you for your understanding and cooperation.
Services: ddbj Keywords: Announcement

Release of TSA and EST data of Botryococcus braunii

July 01,2011
DDBJ newly released TSA and EST data derived from Botryococcus braunii, which had been submitted by National Institute for Environmental Studies.  (Available by getentry)

The accession numbers are as follows ;
  • TSA data    FX056085-FX112549 (56,465 entries)
  • EST data    FY358876-FY368220 ( 9,345 entries)
Services: ddbj Keywords: Announcement

Release of JPO patent nucleotide sequence for 1,591,911 entries

June 24,2011
DDBJ newly released patent nucleotide sequence of 1,591,911 entries submitted from Japan Patent Office (JPO). (Available by getentry)
Accession numbers:



Entry number:
Patent type:

Publication number:
Patent title:
FZ437591 - FZ999999
GB000001 - GB999999
HV000001 - HV029503 1,591,911 entries
Japanese translations of PCT international publication for patent
applications
JP 2006-507841
Functional and Hyperfunctional siRNA
Services: ddbj Keywords: Announcement

(resume) SAKURA suspension for emergency maintenance

June 24,2011
SAKURA is a nucleotide sequence data submission system through the WWW server at DDBJ.
For the urgent maintenance work, SAKURA is suspended at the following schedule.
  • Period: June 24, 2011 (Today) 12:00 - June 27, 2011 (Mon) 10:00 (JST)
Thank you for your understanding and cooperation.
Maintenance works finished, and the service is available. Thank you for your cooperation. (Jun. 27, 2011 at 9:50)
Services: ddbj Keywords: Maintenance

(Jul. 1) ARSA database search temporary unavailable

June 23,2011
ARSA is a high-speed data retrieval system provided by DDBJ via WWW and Web API. DDBJ and DAD database search in ARSA is unavailable in the following schedule to update each of released data (DDBJ Release 86.0 and DAD Release 56.0).
Details are as follows:
  • Date & Time:
      Jul. 1, 2011 (Fri) 9:00 - 24:00 JST (We will announce on this page when the service resumes)
  • Unavailable related services:
      ARSA reference function in TX Search
      DNA/Protein/AllDBs search at the search box of the upper part of DDBJ HP
Thank you for your understanding and cooperation.
Maintenance works finished. Thank you for your cooperation. (Jul. 1, 2011 at 24:00)
Services: ddbj Keywords: Maintenance

DDBJ Rel. 86.0, DAD (DDBJ amino acid database) Rel. 56.0 Completed

June 20,2011
DDBJ Rel. 86.0DAD (DDBJ amino acid database) Rel. 56.0
Services: ddbj Keywords: Announcement

Release of new EST data of tammar wallaby (Macropus eugenii)

June 09,2011
DDBJ newly released EST data derived from tammar wallaby (Macropus eugenii), which had been submitted by National Institute of Genetics.

The accession numbers are as follows ;
  • FY469875-FY736474 (266,600 entries)    (Available by getentry)
Services: ddbj Keywords: Announcement

DBCLS, DDBJ, EMBL-EBI will hold The Bioinformatics Roadshow

June 02,2011
On September 5th and 6th ,DBCLS, DDBJ, EMBL-EBI will hold The Bioinformatics Roadshow in Tokyo (co-hosted by JST-NBDC).
For details, please see here.
Services: ddbj Keywords: Announcement

Resumed ARSA

May 18,2011

Please understand the databases are decreased for electricity conservation.
Available services:
   - DDBJ and DAD search (Search results do not contain 17DBs entries)
   - ARSA reference function in TX Search

Reference: Suspension of a part of the DDBJ services due to the blackout caused by the effect of recent disaster.
Services: ddbj Keywords: Announcement

Release of TPA-WGS and scaffold CON data of vase tunicate

May 11,2011
DDBJ released TPA-WGS and scaffold CON data derived from vase tunicate (Ciona intestinalis) genome, which had been submitted by Kyoto University.


Reference: Ghost Database

The accession numbers are as follows ;
  • TPA-WGS    EAAA01000001 - EAAA01006374 (EAAA.gz) (6,374 entries)
  • TPA-scaffold CON    HT000001 - HT001272 (1,272 entries)    (Available by getentry)
Services: ddbj Keywords: Announcement

Resumed DDBJ Dead Annotation Pipeline

April 27,2011
Services: ddbj Keywords: Announcement

Resumed MiGAP

April 15,2011
Services: ddbj Keywords: Announcement

Temporary delay of a part of the DDBJ services for consecutive holidays

April 14,2011
Days from April 29 to May 8, 2011 are national holidays called Golden Week in Japan. We will at DDBJ suspend our work for releasing data and answering all inquiries during consecutive holidays. Search and analysis and other WWW services are available. We will go back to work as usual from May 9.Thank you for your understanding and cooperation.
Services: ddbj Keywords: Announcement

Resumed BLAST and ClustalW

April 12,2011
Please understand the number of running processes are decreased for electricity conservation.Reference: Suspension of a part of the DDBJ services due to the blackout caused by the effect of recent disaster.
Services: ddbj Keywords: Announcement

Release of new WGS of domesticated barley (Hordeum vulgare) 8,583 entries

April 05,2011
DDBJ newly released WGS sequence data derived from chromosome 3H of domesticated barley (Hordeum vulgare subsp. vulgare cv. Haruna Nijo), which had been submitted by Okayama University.

The accession numbers are as follows ;
  • WGS BACC01000001-BACC01008583 (8,583 entries)

These entries were released as DDBJ daily updates on Apr. 5, 2011.
Services: ddbj Keywords: Announcement

Adding patent number and sequence number on DEFINITION line

March 31,2011
We modified the DEFINITION format of flat file from Japan Patent Office (JPO) and Korean Intellectual Property Office (KIPO).The patent publication/application number and sequence number was set on the head of DEFINITION line.Revision example for DEFINITION line:(Old format)DEFINITION Genetic Makers Expressed in Tumors.(New format)DEFINITION JP 2010599999-A/1: Genetic Makers Expressed in Tumors.We distributed the revised data from following site.(Nucleic acid sequence data)Please get the revised data from Release 85.0 site. They will be reflected sequentially from getentry, ARSA and BLAST.Patent file name: ddbjpat**.seq.gz**: file number(Amino acid sequence data)Please get the revised data from DDBJ anonymous FTP site. They have been already reflected from getentry and BLAST.JPO file: jpo_ddbj_aa.seq.gzKIPO file: kipo_ddbj_aa.seq.gz
Services: ddbj Keywords: Announcement

DDBJ Rel. 85.0, DAD (DDBJ amino acid database) Rel. 55.0 Completed

March 31,2011
DDBJ Rel. 85.0
DAD (DDBJ amino acid database) Rel. 55.0
  • Date: Mar. 30, 2011
  • 19,723,681 entries    5,576,482,211 aa (total number of residues)
  • DAD Release Note
Services: ddbj Keywords: Announcement

Release of GSS data of African rice (Oryza glaberrima)

March 25,2011
DDBJ newly released GSS data derived from African rice (Oryza glaberrima ) 437,642 entries, which had been submitted by National Institute of Agrobiological Sciences.


The accession numbers
are as follows ;
  • FT434720-FT654719 (220,000 entries) released on Mar. 24
  • FT654720-FT872361 (217,642 entries) released on Mar. 25
Services: ddbj Keywords: Announcement

Release of full length cDNA sequence data of domesticated barley (Hordeum vulgare subsp. vulgare)

March 23,2011
DDBJ newly released full length cDNA sequence data derived from domesticated barley (Hordeum vulgare subsp. vulgare ), which had been submitted by National Institute of Agrobiological Sciences.


The accession numbers are as follows ;
  • AK353559-AK377172 (23,614 entries)
These entries were released as DDBJ daily updates on Mar. 18, 2011.
Services: ddbj Keywords: Announcement

Suspension of a part of the DDBJ services due to the effects of recent disaster

March 14,2011
Due to the effects of recent disaster to the major power plants, eastern Japan including us is now under a rolling blackout.The DDBJ services will be affected accordingly.

Service suspension for electricity conservation

Details are as follows:
ServiceSuspended schedule
supernigfrom March 14, 2011(Resuming schedule is not yet determined)
other than abovetemporarily(according to the rolling blackout schedule by TEPCO*,DDBJ and NIG belongs to "Group2 SubgroupE" of rotation group)Group2 SubgroupE blackout schedule:  Suspension schedule caused by the implementation of rolling blackouts 
* TEPCO: Tokyo Electric Power Company
Note:
  • DDBJ Services will be suspended according to the schedule of electric powercut by Tokyo Electric Power Company (TEPCO).
  • DDBJ belongs to "Group2 SubgroupE" in the rotation of elecrtic outage by TEPCO.
  • Please understand all services might be suspended without any prior notices.
  • We plan to receive data submision as usual as possible, but the availability of the reception services and the schedule of data-exchange among EMBL, GenBank, DDBJ may be affected somehow.
  • However, please be aware of unannounced blackout, during your data submission to DDBJ (by SAKURA, MSS, DRA, DTA etc).

Resumed ARSA

Please understand the databases are decreased for electricity conservation. (2011.05.18)
Available services:
   - DDBJ and DAD search (Search results do not contain 18DBs entries)
   - ARSA reference function in TX Search

Resumed BLAST and ClustalW.

Please understand the number of running processes are decreased for electricity conservation. (2011.04.12)

-Resumed MiGAP  (2011.04.15)

-Resumed DDBJ Read Annotation Pipeline  (2011.04.27)

About the service stop according to the rolling blackout

DDBJ 's service suspension is not carried out because the TEPCO decided to cease the implementation of rolling blackouts. (2011.04.11)
Thank you very much for your understanding and cooperation.
March 14, 2011
Services: ddbj Keywords: Maintenance

DDBJ network services is unavailable for power outage

March 09,2011
DDBJ network services including NIG supercomputer (supernig) will be unavailable at the following schedule because of the electric power outage. Please note that the suspended period depends on the service.
ServicesScheduled (JST)
SAKURA, getentry, BLAST, ClustalW,TXSearch, Vector Screening System,GIB, Anonymous-FTPMar.18(Fri) 15:00 - Mar.22(Tue) 12:00
ARSAMar.18(Fri) 15:00 - Mar.22(Tue) 18:00
NIG supercomputer (supernig)Mar.18(Fri) 15:00 - Mar.22(Tue) 9:00
DDBJ HPMar.18(Fri) 17:00 - Mar.22(Tue) 9:00
Thank you for your cooperation and understanding.
Services: ddbj Keywords: Maintenance

Release of new data of rice (Oryza sativa Japonica Group) GSS 59,716 entries

February 25,2011
DDBJ newly released GSS data derived from rice (Oryza sativa Japonica Group ), which had been submitted by National Institute of Agrobiological Sciences.


The accession numbers are as follows ;
  • FT872362-FT932077 (59,716 entries)
These entries were released as DDBJ daily updates on Feb. 25, 2011.
Services: ddbj Keywords: Announcement

(Mar.1) NIG and DDBJ network services temporary down

February 25,2011
NIG (National Institute of Genetics) network service will be unavailable at the following schedule because of the network maintenance. DDBJ network service and NIG supercomputer (supernig) service will also be unavailable.


  • Date: Mar. 1(Tue), 2011 at 19:30 - 21:30 (JST)30 minutes interception during the above time
Thank you for your cooperation.
Services: ddbj Keywords: Maintenance

DAD Rel. 54.1 released

February 23,2011
DAD released Rel.54.1, because a part of trouble had been found in Rel.54 (released on Jan. 2011).


Reference: Apologies for the trouble of in DAD release 54.
 
Services: ddbj Keywords: Announcement

Announcement: DDBJ will continue Sequence Raw Data Archiving

February 22,2011
Services: dra Keywords:

DDBJ will continue Sequence Raw Data Archiving

February 22,2011

DDBJ will continue Sequence Raw Data Archiving

2011/2/22

Contents

DDBJ will continue Sequence Raw Data Archiving

    DDBJ has been archiving raw data from Sanger sequencers and so called next-generation sequencers as a part of EBI/NCBI/DDBJ International Nucleotide Sequence Database Collaboration (INSDC), by receiving data submissions from sequence centers mainly in Japan and also from several other countries.

    The data submitted to DDBJ are processed into INSDC approved format and exchanged among NCBI and EBI frequently to make a same data set in either bank at the timing of data publication to minimize the difference in convenience of data access from all over the world.

    In light of the recent announcement that NCBI, who has been playing a hub in raw data archiving, will discontinue its Sequence Read Archive and Trace Archive repositories, DDBJ's archiving will be affected somehow in the near future.

    However, at this moment, DDBJ does not plan to discontinue either of the service to meet the demand of the domestic community as well as of the global one.

    DDBJ has just started to formulate the plan to minimize the effect to the present activity of INSDC as well as the entire community in collaboration with other INSDC members.

Present status of DDBJ Raw sequence data Archive

  • DDDJ raw data archiving accepts submission of raw data from autosequencers to be shared among the whole community.
  • This is a part of the International Nucleotide Sequence Database Collaboration (INSDC) which is a collaboration among NCBI/EBI/DDBJ.
  • Two types of archiving are provided to accommodate different principles in autosequencers, namely DDBJ Read Archive and DDBJ Trace Archive.

DDBJ Sequence Read Archive(DRA)[2]

  • Raw data from so-called next generation sequencers is the subject for archiving.
    • "A Read File" is data representing chronological color change of a spot [3] which corresponds to extension reaction of one independent molecular species from tens to hundreds of bases.
    • Autosequencers can generate millions or more read files by a single run.
    • Resulting raw data from a single run usually amounts to 100 mega byte to 20-30 giga bytes, which is 1/3 of the disk space in an iPad.

Upon submission to DDBJ

  • Meta data describing the submitters, materials and methods for the reaction as well as read data will become accessible from either of the INSDC collaborators upon publication.
    • DDBJ will first issue a unique accession number for the submission.
    • DDBJ will make metadata in INSDC format and send it to NCBI which is mirrored in all INSDC.
    • DDBJ will create the submitter's account where necessary data are placed by submitters.
    • DDBJ will convert vender specific raw data files into INSDC approved format (SRA format[4]) via NCBI's service.
    • This step will require data transfer using Aspera server in NCBI for mass data transfer.
    • Usually a single submission amounts in the order of 10 runs and transfer of it takes a few seconds to a few hours.
    • Open access data is accumulated in NCBI likewise from EBI, and by copying the entire open access archive from NCBI frequently, the one same open access dataset is made available from any of the three INSDC sites.
    • The size of the data stored only in one bank depends on the amount of submitted, but unpublished data as well as the personal genome data shared under control by researcher groups.
    • This fraction is usually much more than open access data and NCBI has by far a bigger amount than DDBJ.

The size of the DRA

  • As of last week, users can search, browse and download 95,388 runs of open access data from DDBJ.
    • This amounts to 71 tera bytes in the SRA-lite format which lacks only the intensity data found in the SRA format.
    • 71 tera bytes is a disk space of almost one thousand iPads.
    • Submitted but embargo data in DDBJ amounts to 721 runs, which occupies a few tera bytes.
    • DDBJ allocates 273 tera bytes for this service which is planned to be increased in two steps up to 20 peta bytes in the coming 24 months.

Trace Archive at DDBJ (DTA)[5]

  • Trace Archive service accepts submission of raw data generated from autosequencers using Sanger reaction to be shared by the entire community.
    • Trace file is a chronological change of color intensities along a single capillary gel or a lane in a gel plate [6]
    • A typical autosequencer generates dozens to a few hundreds of such data by a single run.
    • A trace is a few hundred bases long and amounts to a few hundred kilo bytes.

Upon submission to DDBJ

  • Meta data describing experimental background becomes searchable and trace data becomes browsable and downloadable from all INSDC collaborators.
    • DDBJ will help generate meta-data file in an INSDC approved format.
    • DDBJ will create a submitter's account where necessary data are placed by submitters.
    • DDBJ will transfer the data to NCBI and NCBI will issue the unique identifier for the service.
    • DDBJ will store and serve only the trace data submitted to DDBJ.
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DDBJ Rel. 84.1 released

February 22,2011
DDBJ released Rel.84.1, because a part of trouble had been found in Rel.84 (released on Dec. 2010).


Reference: Apologies for the trouble of in DDBJ release 84.
 
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Apologies for the trouble of in DAD release 54

February 10,2011
In DAD release 54(released on Jan. 2011), trouble was found in a part. Details are as follows:


  • Situation: The data that had to be excluded was included.
  • Services: Anonymous FTP, ARSA, Homology Search, NIG supercomputer(supernig)
  • Measure: DDBJ will releases "DAD release 54.1".
Corresponding Files:
 BCT (44 entries)  / ddbjbct2.DAD.gz, ddbjbct10.DAD.gz HUM (13 entries)  
/ ddbjhum.DAD.gz INV (9 entries)   / ddbjinv2.DAD.gz PLN (1 entry)     
/ ddbjpln2.DAD.gz SYN (1 entry)     / ddbjsyn.DAD.gz VRL (44 entries)  
/ ddbjvrl1.DAD.gz  VRT (274 entriesWe apologize for your inconvenience. 
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Whole genome sequencing data of sake-brewing Japonica rice Omachi is released.

February 09,2011
Whole genome sequencing data DRA000307 of sake-brewing Japonica rice Omachi (Oryza sativa Japonica Group, cultivar Omachi) submitted by the Tokyo Univetsity of Agriculture have been released. SNP information is available at the NGRC_Rice_Omachi Genome Browser by the Tokyo Univetsity of Agriculture.
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Apologies for the trouble of in DDBJ release 84

February 07,2011
In DDBJ release 84(released on Dec. 2010), trouble was found in a part. Details are as follows:


  • Situation: The data that had to be excluded was included.
  • Services: Anonymous FTP, ARSA, Homology Search, DAD, NIG supercomputer(supernig)
  • Measure: DDBJ will releases "DDBJ release 84.1".
Corresponding Files:
 BCT (33 entries)  / ddbjbct2.seq.gz, ddbjbct8.seq.gz, ddbjbct9.seq.gz ENV (217 entries) /
 ddbjenv4.seq.gz, ddbjenv5.seq.gz EST (1 entry)     / ddbjest145.seq.gz HUM (21 entries)  
/ ddbjhum6.seq.gz INV (9 entries)   / ddbjinv4.seq.gz PLN (2 entries)   
/ ddbjpln5.seq.gz, ddbjpln7.seq.gz ROD (27 entries)  / ddbjrod5.seq.gz SYN (1 entry)     
/ ddbjsyn.seq.gz VRL (33 entries)  / ddbjvrl1.seq.gz,  VRT (403 entries)
 / ddbjvrt1.seq.gz, ddbjvrt3.seq.gz, ddbjvrt4.seq.gz CON (16,633 entries) 
/ ddbjcon5.seq.gz, ddbjcon6.seq.gz, ddbjcon7.seq.gz, ddbjcon8.seq.gz, ddbjcon11.seq.gz
We apologize for your inconvenience.
Services: ddbj Keywords: Maintenance

Release of new mouse (Mus musculus domesticus) GSS 131,507 entries

February 07,2011
DDBJ newly released 131,507 entries of GSS data derived from mouse (Mus musculus domesticus ), which had been submitted by RIKEN BioResource Center.


The accession numbers  (Anonymous FTP)  are as follows ;Reference URL: RIKEN BioResource Center DNA BANK
These entries were released as DDBJ daily updates on Feb. 5, 2011.
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DDBJ/EMBL/GenBank Feature Table Definition revised

February 04,2011
Feature Table Definition(FT-Doc) 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. Following the decision at an International Collaborators Meeting(ICM) held annually in May, this FT-Doc is updated every year. In January 2011, FT-Doc is updated, based on the 23rd International Collaborators Meeting.
Services: ddbj Keywords: Announcement

(Jan.28) ARSA database search (DDBJ, DAD) temporary unavailable

January 24,2011
ARSA is a high-speed data retrieval system provided by DDBJ via WWW and Web API. DDBJ and DAD database search in ARSA is unavailable in the following schedule to update each of released data (DDBJ Release 84.0 and DAD Release 54.0. Details are as follows:
  • Date & Time:  Jan. 28, 2011 (Fri) 9:00 - 21:00 JST (We will announce on this page when the service resumes)
  • Unavailable services:  DDBJ and DAD search in ARSA (another 17DBs are searchable. Search results do not contain DDBJ and DAD entries)  ARSA reference function in TX Search  DNA/Protein/AllDBs search at the search box of the upper part of DDBJ HP (another DB search are available)
Thank you for your understanding and cooperation.
Maintenance works finished. Thank you for your cooperation. (Jan. 28, 2011 at 16:30)
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Report for DDBJ activities in NAR

January 21,2011
DDBJ activities were introduced in the following papers appeared in Nucleic Acids Research Vol.39 Database Issue (Jan.2011).


"The International Nucleotide Sequence Database Collaboration"Guy Cochrane, Ilene Karsch-Mizrachi, and Yasukazu Nakamura on behalf of the International Nucleotide Sequence Database Collaboration.Nucleic Acids Research, 2011, Vol. 39, Database issue D15-D18"The Sequence Read Archive"Rasko Leinonen, Hideaki Sugawara, and Martin Shumway on behalf of the International Nucleotide Sequence Database Collaboration.Nucleic Acids Research, 2011, Vol. 39, Database issue D19-D21"DDBJ progress report"Eli Kaminuma, Takehide Kosuge, Yuichi Kodama, Hideo Aono, Jun Mashima, Takashi Gojobori, Hideaki Sugawara, Osamu Ogasawara, Toshihisa Takagi, Kousaku Okubo, and Yasukazu Nakamura.Nucleic Acids Research, 2011, Vol. 39, Database issue D22-D27
 
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DAD (DDBJ amino acid database) Rel. 54.0 Released

January 14,2011
Services: ddbj Keywords: Announcement

ARSA database search (DDBJ, DAD) temporary unavailable

January 12,2011
(This was postponed. Today is usual.)ARSA is a high-speed data retrieval system provided by DDBJ via WWW and Web API. DDBJ and DAD database search in ARSA is unavailable in the following schedule to update each of released data (DDBJ Release 84.0, DAD Release 54.0 will be released on Jan. 14, 2011.) Details are as follows:
  • Date & Time:  Jan. 21, 2011 (Fri) 9:00 - 18:00 JST (We will announce on this page when the service resumes)
  • Unavailable services:  DDBJ and DAD search in ARSA (another 17DBs are searchable. Search results do not contain DDBJ and DAD entries)  ARSA reference function in TX Search  DNA/Protein/AllDBs search at the search box of the upper part of DDBJ HP (another DB search are available)
Thank you for your understanding and cooperation.
Services: ddbj Keywords: Maintenance

Release of new whole genome and cDNA sequence data of a biofuel crop, Jatropha curcas

January 11,2011
DDBJ newly released whole genome and cDNA sequence data of a biofuel crop, Jatropha curcas, which had been submitted by the Kazusa DNA Research Institute.


Reference URL:
The accession numbers (Anonymous FTP download) are as follows;
Services: ddbj Keywords: Announcement

Release of new EST data of a flatworm (Clonorchis sinensis)

January 11,2011
DDBJ newly released EST data derived from a flatworm (Clonorchis sinensis), which had been submitted by Korea Research Institute of Bioscience and Biotechnology.


The accession numbers are as follows;
  • FS126466-FS179210 (52745 entries)
Services: ddbj Keywords: Announcement

DRA directory composition of FTP was changed

January 07,2011
dra directory composition of DDBJ FTP site was changed.The data which had been placed under /ddbj_database/dra are available in "fastq", and SRA lite formatted data are newly available in "sralite". SRA lite contains sequence and fastq data.For details, please see README.TXT. If you automatically monitor DDBJ anonymous FTP, please confirm your monitoring program if necessary.
Services: ddbj Keywords: Announcement

Whole genome sequencing and cDNA data of biodiesel-producing Jatropha are released.

January 06,2011
Whole genome sequencing (DRA000305 and DRA000306) and cDNA (DRA000303 and DRA000304) data of biodiesel-producing Jatropha (Jatropha curcas) submitted by the KAZUSA DNA Research Institute have been released. » press release by KAZUSA (Japanese).
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SRA Lite format data is available on the FTP site.

January 05,2011
SRA Lite format data is available on the FTP site. Please refer to the NCBI SRA Handbook for the SRA format data.
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