DDBJ Center News Archive

News from 2014

DDBJ Rel. 99.0, DAD Rel. 69.0 Completed

2014年12月25日

DDBJ Rel. 99.0

DAD (DDBJ amino acid database) Rel. 69.0
  • Date: Dec. 25, 2014
  • 36,947,790 entries     11,288,302,791 aa (total number of residues)
  • DAD Release Note
Services: ddbj Keywords: Data Release

Suspension of the DDBJ activity during the New Year Holidays

December 24,2014

We at DDBJ will temporarily close for the New Year Holidays from December 27(Sat) 2014 to January 4(Sun) 2015.
Please note that DDBJ Nucleotide Sequence Submission System will be unavailable. Schedule is as follows.
NIG SuperComputer and DDBJ network services (except DDBJ Nucleotide Sequence Submission System)
are available during the New Year Holidays.

During this period, DDBJ will continue to receive inquiries from E-mail and "Contact" web form.
But, please note that replies from DDBJ is after the reopening of the office in January, 2015.

DDBJ office closeDec. 27(Sat), 2014 - Jan. 4(Sun), 2015
DDBJ Nucleotide Sequence Submission SystemDec. 25(Thu), 2014 at 17:00
     - Jan. 5(Mon), 2015 at 10:00(JST)
Data release suspensionDec. 25(Thu), 2014 - Jan. 5(Mon), 2015
Reply for inquiries
(submission, search/analysis, NIG SuperComputer)
Dec. 27(Sat), 2014 - Jan. 4(Sun), 2015
DRA, BioProject, BioSample, JGA Accession No. issueDec. 27(Sat), 2014 - Jan. 4(Sun), 2015

Thank you for your understanding and cooperation.

ecember 10, 2014

Services: ddbj Keywords: Announcement

Report for DDBJ activity in NAR

December 24,2014

DDBJ activity is introduced in the following article appeared in Nucleic Acids Research, Database issue.
The following article will be published on January 1, 2015, and published online on December 3, 2014.

"The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data"
Yuichi Kodama, Jun Mashima, Takehide Kosuge, Toshiaki Katayama, Takatomo Fujisawa, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Toshihisa Takagi, and Yasukazu Nakamura
Nucl. Acids Res. 2014 doi:10.1093/nar/gku1120

 DDBJ activity publications

Services: ddbj Keywords: Announcement

(Jan. 15) Important Notification regarding Nucleotide Sequence Submission System (NSSS)

December 22,2014

DDBJ Nucleotide Sequence Submission System (NSSS) will be unavailable due to the system update from 10:00 January 15(Thu), 2015 (JST).

After the update, all the data that you have selected/entered on the "6. Template" and "7. Annotation" pages are erased.
We would like to ask you to finish the submission by January 15(Thu), 2015 at 10:00 (JST).

If you cannot complete the submission, you must start again from "6. Template" page.

 System Update Schedule
   January 15(Thu), 2015 at 10:00 (JST) Service will be stopped for the system version up.
   January 15(Thu), 2015 at 13:00 (JST) Service will be resumed.

Thank you for your understanding and patience.

Services: ddbj Keywords: Announcement

HOLIDAY CLOSING NOTICE

December 22,2014
Please be informed that, for the new year's holidays, we will be closing from 27th Dec. 2014 until 4th Jan. 2015.
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, BioProject, BioSample, JGA.
We regret any inconvenience this may cause and appreciate your kind understanding.
Services: bioproject,biosample,dra,dta,jga Keywords: Announcement

Changed the update timing of cumulated files for amino acid sequence data from patent offices

December 19,2014
DDBJ provides amino acid (AA) sequence data transferred from Japan Patent Office (JPO) and Korean Intellectual Property Office (KIPO) as cumulated files at following site.
ftp://ftp.ddbj.nig.ac.jp/ddbj_database/patent/

Since December 2014, DDBJ has changed the update timing of cumulated files from every three months to followings.
 [1] JPO data (Once or twice per month)
 [2] KIPO data (Twice per year)
 [3] JPO/KIPO data update or other process (Irregular date)

AA sequence data can be also retrieved through getentry by accession number and through ARSA by keyword.
Services: ddbj Keywords: Announcement

Release of transcriptome sequence data of Raphanus sativus var. sativus, Brassica rapa subsp. pekinensis and their hybrid

December 17,2014

DDBJ released transcriptome sequence data of Raphanus sativus var. sativus, Brassica rapa subsp. pekinensis and their hybrid (Brassica rapa x Raphanus sativus), which had been submitted by Seoul National University.

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

Raphanus sativus var. sativus
    TSA: FX657517-FX691702 (34,186 entries)
    DRA run: DRR014232, DRR014233

Brassica rapa subsp. pekinensis
    TSA: FX691703-FX725989 (34,287 entries)
    DRA run: DRR014230, DRR014231

Brassica rapa x Raphanus sativus
    TSA: FX725990-FX799344 (73,355 entries)
    DRA run: DRR014228, DRR014229

Services: ddbj Keywords: Data Release

Release of genome and transcriptome sequence data of hops (Humulus lupulus), 2 varieties

December 16,2014

DDBJ released genome and transcriptome sequence data of hops (Humulus lupulus), 2 varieties, which had been submitted by Suntory Global Innovation Center Limited.

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

Humulus lupulus var. cordifolius
    scaffold CON: LD000001-LD132476 (132,476 entries)
    WGS: BBPB01000001-BBPB01292698 (BBPB.gz) (292,698 entries)
    DRA run: DRR024452-DRR024456

Humulus lupulus var. lupulus
    scaffold CON: LD132477-LD264952 (132,476 entries)
    WGS: BBPC01000001-BBPC01292698 (BBPC.gz) (292,698 entries)
    DRA run: DRR024392-DRR024447

Humulus lupulus var. lupulus
    TSA: LA328023-LA715951 (387,929 entries)
    DRA run: DRR024457-DRR024463

Services: ddbj Keywords: Data Release

URL Change of TXSearch

December 16,2014
DDBJ provides a taxonomy database retrieval system called TXSearch, to refer taxonomic names of organisms for your submission of nucleotide sequences to DDBJ.
DDBJ changed the URL and the interface of TXSearch.The former URL will not work after December 31, 2014. So, please change your bookmark, etc. at your earliest convenience.http://ddbj.nig.ac.jp/tx_search/
txhelp01_top-eFor the detailed explanation, please refer to the ,"TXSearch Help" page.
DDBJ will continue to improve our services. Your reviews 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

Services are now available

December 04,2014
Now DDBJ center's services are available.
Services: bioproject,biosample,gea,dra,dta,jga Keywords: Maintenance

Feature Table Definition revised

November 21,2014

The DDBJ/ENA/GenBank Feature Table Definition is the common annotation manual of feature descriptions for DDBJ, ENA and GenBank.
It was revised to version 10.4 in November 2014.

Services: ddbj Keywords: Announcement

Web services will be unavailable (18th, Nov. 9:30-10:30)

November 13,2014
Due to maintenance of the BioProject system, web services (search and D-way submission services) will be unavailable (18th, Nov. 9:30-10:30).
Services: bioproject,biosample,gea,dra,dta,jga Keywords: Maintenance

BioSample attributes' names and order were changed

November 12,2014
For clarity, names and order of the BioSample attributes were changed. Please see the list of attributes.
Services: biosample Keywords: Announcement

A BioProject record can have multiple project data types

November 12,2014
By selecting multiple Project Data Types (for example, "Genome Sequencing" and "Transcriptome or Gene Expression"), multiple studies can be merged into single project.
Services: bioproject Keywords: Announcement

Updated tools related to Mass Submission System (MSS)

November 07,2014

DDBJ updated tools related to Mass Submission System.

  • Utilities for MSS file Error check (UME) version 1.37 Released
  • Parser version 6.50 Released
  • transChecker version 2.17 Released

See MSS Home in detail.

Services: ddbj Keywords: Announcement

(Nov. 28 – Dec. 4) DDBJ services will be unavailable

November 05,2014
DRA,BioProject,BioSample,JGA services will be unavailable because of the electric power outage of National Institute of Genetics. Schedule is here.
Services: bioproject,biosample,gea,dra,dta,jga Keywords: Maintenance

Scheduled maintenance (9:30-14:00, 12 Nov.)

November 04,2014
From 9:30 to 14:00, Wednesday, 12th, November, the DRA, BioProject and BioSample submission and search services will be unavailable due to scheduled maintenance.
Services: bioproject,biosample,gea,dra,dta Keywords: Maintenance

(Nov. 28 - Dec. 4) DDBJ network services and NIG Supercomputer will be unavailable (all service resumed)

November 04,2014

NIG Supercomputer and DDBJ network services will be unavailable because of the electric power outage of the NIG(National Institute of Genetics). Schedule is as follows:

ServicesSchedule (JST)
・D-way
・DRA Search
・BioProject Search
・BioSample Search
・JGA Submission/Download Tool
・JGA Meta Viewer
Nov. 28 (Fri) 13:00 - Dec. 4 (Thu) 10:00 (JST)
・NIG SupercomputerNov. 28 (Fri) 17:00 - Dec. 3 (Wed) 24:00 (JST)
・DDBJ anonymous FTP
・getentry
・ARSA
・DDBJ Nucleotide Sequence Submission System
・BLAST
・ClustalW
・DDBJ Read Annotation Pipeline
・MiGAP
・DDBJ Homepage
Nov. 28 (Fri) 17:00 - Dec. 4 (Thu) 10:00 (JST)

Thank you for your understanding and cooperation.

All services are available. (December 4, 2014)
Thank you for your cooperation.

Services: ddbj Keywords: Maintenance

(10/24) Session interruption due to the web server restart

October 23,2014

DDBJ web server will be restarted to change its configurations as follows.
During this time period, session can be interrupted.

 October 24 (Fri.), 14:00 - 15:00 (JST)

DDBJ web services
・D-way
・DRA Search
・BioProject Search
・NIG SuperComputer
・DDBJ HP
・getentry
・ARSA
・DDBJ Nucleotide Sequence Submission System
・BLAST
・ClustalW
・DDBJ Read Annotation Pipeline
・MiGAP
・MiGAP-OLD

Thank you for your understanding and cooperation.

Services: ddbj Keywords: Maintenance

Possible session interruption due to the web server restart

October 23,2014
During 14:00-15:00, 24th October (Friday), the DDBJ web server will be restarted to change its configurations. During this time period, session can be interrupted.
Services: bioproject,biosample,gea,dra,dta,jga Keywords: Maintenance

Apologies for defects in FASTA, XML and blast db files including HG670306 and HG975440

October 15,2014

Some disorders were found in software tools to convert sequence data from flat file to FASTA or XML formats.
Because of the disorders, the data with over 100,000,020 bp in the sequence length (HG670306 and HG975440) lacked their parts of sequences in FASTA and XML formats.
Details are as follows:

Period:
From 2014.10.02 to 2014.10.12
Services:
Anonymous FTP, BLAST
Situation:
Incorrect sequences were included in FASTA, XML and blast db files;
    dbjpln10.fasta.gz (FASTA '~/ddbj/fasta' directory)
    dbjpln10.fasta.gz (FASTA '~/ddbjnew/unified-all/fasta' directory)
    ddbjpln10.insd_xml.gz (XML '~/ddbj/xml/insdxml/v1.4' directory)
    pln.tar.gz (blast db '~/ddbjnew/unified-all/blastdb' directory)
Measure:
We replaced the files to correct ones and applied for our BLAST service.

We apologize for your inconvenience.

Services: ddbj Keywords: Announcement

Validation and data release processings are busy

October 14,2014
At present, because large number of files are submitted, the validation and data release systems are busy. Submissions with status "prepare" and "data_validating" are in validation process queue. Please wait a little while more.
Services: dra Keywords:

Submission system will be unavailable.

October 10,2014
Submission system will be unavailable due to the hard disk troubles. If restored, we will announce.
Services: jga Keywords: Maintenance

Scheduled maintenance (9:30-14:00, 8 Oct.)

October 03,2014
From 9:30 to 14:00, Wednesday, 8th, October, the DRA, BioProject and BioSample submission and search services will be unavailable due to scheduled maintenance.
Services: bioproject,biosample,dra Keywords: Maintenance

DDBJ Rel. 98.0, DAD Rel. 68.0 Completed

October 02,2014

DDBJ Rel. 98.0

DAD (DDBJ amino acid database) Rel. 68.0
  • Date: Oct. 2, 2014
  • 35,066,241 entries     10,653,219,680 aa (total number of residues)
  • DAD Release Note
Services: ddbj Keywords: Data Release

Scheduled maintenance (9:30-14:00, 25 Sep.)

September 22,2014
From 9:30 to 14:00, Thursday, 25th, September, the DRA, BioProject and BioSample submission and search services will be unavailable due to scheduled maintenance.
Services: bioproject,biosample,dra Keywords: Maintenance

Sample title is required for all sample type

September 18,2014
Sample title became a mandatory attribute for all sample type from 16:30 on September 18, 2014. Please upload the file with sample title if an error occurs.
Services: biosample Keywords: Announcement

Release of genome sequence data of eggplant (Solanum melongena)

September 18,2014

DDBJ released genome sequence data of eggplant (Solanum melongena), which had been submitted by Kazusa DNA Research Institute.

Reference;
Eggplant Genome DataBase

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

    scaffold CON: DF357214-DF384212 (26,999 entries)
    WGS: BAUE01000001-BAUE01143048 (BAUE.gz) (143,048 entries)
    SRA: DRR014074-DRR014076

Services: ddbj Keywords: Data Release

Add links to DBCLS search tools

September 12,2014

Links to the Search tools developed and maintained by Database Center for Life Science (DBCLS) was added to the "Search and Analysis" in this web site.

Services: ddbj Keywords: Announcement

Mirroring has been stopped due to insufficient disk volume

September 09,2014
Because disk space of the DRA file server is not enough, mirroring with the NCBI SRA has been stopped. The list of available mirrored fastq files: fastqlist
Services: dra Keywords:

Updated tools related to Mass Submission System (MSS)

September 05,2014

DDBJ updated tools related to Mass Submission System.

  • Utilities for MSS file Error check (UME) version 1.36 Released
  • Parser version 6.49 Released
  • transChecker version 2.16 Released

See MSS Home in detail.

Services: ddbj Keywords: Announcement

The Report for the 27th International Collaborators Meeting

September 04,2014

International Nucleotide Sequence Database Collaboration (INSDC), consisted of DDBJ, EBI and NCBI, hold the international collaborators meeting every year.
In 2014, the meeting was held at DDBJ, 20-22 May, to discuss practical matters to maintain and update nucleotide sequence data archives; DDBJ, ENA, GenBank, Sequence Read Archive (SRA) and Trace Archive.
The outcomes of the meeting are summarized here.

Services: ddbj Keywords: Announcement

[DRA, BioProject, BioSample] System is now available

August 25,2014

DRA, BioProject, and BioSample submission/search services are now available. Sorry for the inconvenience.

Services: ddbj Keywords: Maintenance

System is now available

August 25,2014
The submission and search services for DRA, BioProject, and BioSample are now available. These services were restored from system problem. We apologize for causing you the trouble.
Services: bioproject,biosample,gea,dra,dta,jga Keywords: Maintenance

[DRA, BioProject, BioSample] System temporarily unavailable

August 25,2014

At present, DRA, BioProject and BioSample submission and search services are temporarily unavailable because of hardware problem. Since we are looking into the cause of this system failure, please follow our twitter @DDBJ_topics and wait the announcement of recovery.

Services: ddbj Keywords: Maintenance

System temporarily unavailable

August 25,2014
At present, DRA, BioProject and BioSample submission and search services are temporarily unavailable because of hardware problem. Since we are looking into the cause of this system failure, please follow our twitter @DDBJ_topics and wait the announcement of recovery.
Services: bioproject,biosample,gea,dra,dta,jga Keywords: Maintenance

SUMMER HOLIDAY CLOSING NOTICE

August 13,2014
Please be informed that, for the summer holiday, we will be closing from 14th until 15th Aug. 2014.
However, we will continue to accept online submissions via D-way and searches for DRA, BioProject, and BioSample.
Services: bioproject,biosample,gea,dra,dta,jga Keywords: Announcement

Web submission system loads fastq files with variable read length

August 06,2014

The DRA web submission system can load fastq files with variable read length. Handbook.

·fastq files with constact read length: Select fastq in the file type of Run.
·fastq files with variable read length: Select generic_fastq in the file type of Run.
Services: dra Keywords: Announcement

(8/14-15) Suspension of some parts of DDBJ activities during summer holidays

August 05,2014

DDBJ will suspend our business on releasing data and answering inquiries from August 14 to August 15, 2014(JST) due to NIG summer holidays. We will reply to your messages on or after August 18. But, all WWW services are available.

    Thursday, August 14, 2014 - Friday, August 15, 2014 (JST)

Thank you for your understanding and cooperation.

Services: ddbj Keywords: Announcement

Revision announcement for publication number of International patent publication data

August 05,2014
DDBJ opens Nucleotide sequence data and Amino acid sequence data for International patent publication submitted from Japan Patent Office (JPO).

(1) Publication number format
Current format of publication number for International patent publication data (WO data) is constructed as follows.

 Format:  WO [4 digit year][6 digit ID]
 Example: WO 2014123456
 *WO of publication number is the country code for WIPO (World Intellectual Property Organization).

In case of WO data submitted in 2000-2003, publication number was constructed as last two number of the year and 5 or 6 digit ID.

 Format:  WO [2 digit year][5 or 6 digit ID]
 Example: WO 01123456
               WO 0112345

(2) Revision contents
DDBJ revised the publication number of different format as current format with the cooperation of JPO, to improve retrieval convenience for user by publication number.

 Revision example: WO 01123456 --[correction]-> WO 2001123456
                           WO 0112345  --[correction]-> WO 2001012345

Revised WO data has been already distributed from getentry and ARSA.

 Nucleotide sequence data (39,737 entries WOna_list):
 [Data example]
 http://getentry.ddbj.nig.ac.jp/getentry/na/BD091582


 Amino acid sequence data (11,460 entries WOaa_list):
 [Data example]
 http://getentry.ddbj.nig.ac.jp/getentry/patent_aa/BD649684

Services: ddbj Keywords: Announcement

[DRA, BioProject, BioSample] Scheduled maintenance

August 05,2014

From 9:30 to 11:00, Wednesday, 6th, August, the DRA, BioProject and BioSample submission and search services will be unavailable due to scheduled maintenance.

Services: ddbj Keywords: Maintenance

Validation processings are busy

August 05,2014
At present, because large number of files are submitted, the validation system is busy. Submissions with status "prepare" and "data_validating" are in validation process queue, please wait for the validation finishes without stopping the validation.
Services: dra Keywords:

(8/5) ARSA temporarily unavailable (Resumed)

August 04,2014

ARSA will be unavailable due to NIG Supercomputer maintenance as follows.

 August 5 (Tue.), 13:00 - 16:00 (JST)
tentative schedule

Thank you for your understanding and cooperation.

NIG Supercomputer maintenance finished. ARSA is available.
Thank you for your cooperation.

Services: ddbj Keywords: Maintenance

Scheduled maintenance

August 01,2014
From 9:30 to 11:00, Wednesday, 6th, August, the DRA, BioProject and BioSample submission and search services will be unavailable due to scheduled maintenance.
Services: bioproject,biosample,gea,dra,dta Keywords: Maintenance

System is now available

July 15,2014

DDBJ Nucleotide Sequence Submission System and DRA, BioProject, BioSample submission/search services are now available. These services were restored from hardware problem.

DDBJ sincerely apologize for your inconvenience.

Services: ddbj Keywords: Maintenance

System is now available

July 15,2014
The submission and search services for DRA, BioProject, and BioSample are now available. These services were restored from hardware problem. We apologize for causing you the trouble.
Services: bioproject,biosample,gea,dra,dta,jga Keywords: Maintenance

(Today) System temporarily unavailable

July 14,2014

At present, DDBJ Nucleotide Sequence Submission System, DRA, BioProject and BioSample submission
and search services(DRA Search, BioProject Search, BioSample Search) are temporarily unavailable because of hardware problem.

Since we are looking into the cause of this system failure,
please follow our twitter @DDBJ_topics and wait the announcement of recovery.

Thank you for your understanding and cooperation.

Services: ddbj Keywords: Maintenance

System temporarily unavailable

July 14,2014
At present, DRA, BioProject and BioSample submission and search services are temporarily unavailable because of hardware problem. Since we are looking into the cause of this system failure, please follow our twitter @DDBJ_topics and wait the announcement of recovery.
Services: bioproject,biosample,gea,dra,dta,jga Keywords: Maintenance

Data release of patent sequence from Korean Intellectual Property Office (KIPO)

July 08,2014
DDBJ distributed the patent sequence data submitted from Korean Intellectual Property Office (KIPO).
KIPO data was issued the accession number as follows.
Nucleotide sequence data (122,339 entries): DI246931-DI369269
Amino acid sequence data (43,308 entries): DI661182-DI704489
They are available on getentry.
Please check KIPO data example at following URL.
Example of Nucleotide sequence data:
http://getentry.ddbj.nig.ac.jp/getentry/na/DI246931
Example of Amino acid sequence data:
http://getentry.ddbj.nig.ac.jp/getentry/aa/DI661182
Submission files were processed and submitted to DDBJ by Dr. Byungwook Lee at Korean Bioinformation Center (KOBIC) in collaboration with KIPO.
Services: ddbj Keywords: Data Release

Scheduled maintenance

July 04,2014
From 9:30 to 11:30, Wednesday, July 9th, the DRA, BioProject and BioSample submission and search services will be unavailable due to scheduled maintenance.
Services: bioproject,biosample,gea,dra,dta,jga Keywords: Maintenance

Release of EST data of cellular slime mold (Acytostelium subglobosum)

July 03,2014

DDBJ released EST data derived from a kind of cellular slime mold (Acytostelium subglobosum), which had been submitted by University of Tsukuba.

Reference: Acytostelium Gene Database

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

HY448297-HY457975 9,679 entries 5'-EST vegetative stage
HY457976-HY467594 9,619 entries 3'-EST vegetative stage
HY467595-HY470588 2,994 entries 5'-EST vegetative stage
HY470589-HY473646 3,058 entries 3'-EST vegetative stage
HY473647-HY491366 17,720 entries 5'-EST developmental stage
HY491367-HY508708 17,342 entries 3'-EST developmental stage
total 60,412 entries  
Services: ddbj Keywords: Data Release

Introduction of Statistics of Submissions to DDBJ

July 03,2014

We open a new web site to show statistics of sequence data submissions to DDBJ.
It visualizes DDBJ activities mainly based on number of times to load submitted data to DDBJ.

Monthly Data Submitter and Session to DDBJ

Services: ddbj Keywords: Announcement

FAQ renewal

June 27,2014
Q and A was renewed and the name changed to FAQ. Please use it.FAQ:http://www.ddbj.nig.ac.jp/faq/
Services: ddbj Keywords: Announcement

Updated tools related to Mass Submission System (MSS)

June 26,2014

DDBJ updated tools related to Mass Submission System.

  • Utilities for MSS file Error check (UME) V1.35 Released
  • transChecker V2.15 Released

See MSS Home in detail.

Services: ddbj Keywords: Announcement

DDBJ Rel. 97.0, DAD Rel. 67.0 Completed

June 19,2014

DDBJ Rel. 97.0

DAD (DDBJ amino acid database) Rel. 67.0
  • Date: Jun. 19, 2014
  • 33,234,287 entries     10,031,547,300 aa (total number of residues)
  • DAD Release Note
Services: ddbj Keywords: Data Release

BLAST web design renewal

June 13,2014

BLAST web design renewal.
All other functions remain unchanged.

Please use it.

Services: ddbj Keywords: Announcement

(Jun. 23-26) DDBJ network services and NIG Supercomputer will be unavailable (all service resumed)

June 13,2014

DDBJ network services and NIG Supercomputer will be unavailable because of the NIG Supercomputer's maintenance.
Schedule is as follows:

[make_table title=yes title_font_weight=bold color="#c9c0bb" set_width=650px]ServicesSchedule (JST)・D-way
・DRA Search
・BioProject Search
・BioSample Search
・DDBJ Read Annotation PipelineJune 23(Mon) 13:00 - June 26(Thu) 12:00 (JST)・DDBJ HomepageJune 23(Mon) 17:00 - June 25(Wed) 9:00 (JST)・DDBJ anonymous FTP
・getentry
・ARSA
・DDBJ Nucleotide Sequence Submission System
・BLAST
・ClustalW
・MiGAPJune 23(Mon) 17:00 - June 26(Thu) 9:00 (JST)・NIG SupercomputerJune 24(Tue) 8:00 - June 25(Wed) 24:00 (JST)[/make_table]

Thank you for your understanding and cooperation.

All services are available. (June 26, 2014 at 15:00 JST)
Thank you for your cooperation.

Services: ddbj Keywords: Maintenance

System temporarily unavailable

June 11,2014
From 13:00 June 23th (Mon) until 12:00 June 26th (Thu), DRA, BioProject and BioSample submission and search services will be unavailable because of the NIG super computer's maintenance.
Services: bioproject,biosample,gea,dra,dta,jga Keywords: Maintenance

Release of TSA data of intestinal metagenome of grass carp (Ctenopharyngodon idella)

June 09,2014

DDBJ released TSA (Transcriptome Shotgun Assembly) data derived from intestinal metagenome of grass carp (Ctenopharyngodon idella), which had been submitted by Institute of Hydrobiology, Chinese Academy of Sciences.

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

TSA SRA
LA000001-LA022570 DRR013890
LA022571-LA050083 DRR013891
LA050084-LA080192 DRR013892
LA080193-LA098774 DRR013893
LA098775-LA118857 DRR013894
LA118858-LA151643 DRR013895
LA151644-LA221552 DRR013896
LA221553-LA244919 DRR013897
LA244920-LA284088 DRR013898
LA284089-LA296882 DRR013899
LA296883-LA328022 DRR013900
Services: ddbj Keywords: Data Release

Periodic system maintenance

June 09,2014
From 9:30 to 11:00, Wednesday, June 11, DRA, BioProject and BioSample submission and search services will be unavailable because of periodic system maintenance.
Services: bioproject,biosample,gea,dra,dta,jga Keywords: Maintenance

Release of genome sequence data of radish (Raphanus sativus), 8 cultivars

June 06,2014

DDBJ released genome sequence data of radish (Raphanus sativus), 8 cultivars, which had been submitted by Kazusa DNA Research Institute.

Reference;
Database: Raphanus sativus Genome DataBase
Academic paper: Draft Sequences of the Radish (Raphanus sativus L.) Genome

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

Raphanus sativus cv. Aokubi S-h
    scaffold CON: DF384214-DF396802 (12,589 entries)
    WGS: BAUK01000001-BAUK01101710 (BAUK.gz) (101,710 entries)
    GSS: GA872392-GA901611 (29,220 entries)

raw data
cultivar SRA
Raphanus sativus cv. Aokubi S-h DRR014095, DRR014096, DRR014097
Raphanus sativus cv. Sayatori DRR014098
Raphanus sativus cv. Taibyosobutori DRR015470
Raphanus sativus cv. Yumehomare DRR015471
Raphanus sativus cv. Sakurajima DRR015472
Raphanus sativus cv. AZ26H DRR015473
Raphanus sativus cv. N1-3 DRR015474
Raphanus sativus cv. Nishimachi-Risou DRR015475
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[DRA] System is now available

June 02,2014

The DRA search service "DRAsearch" and FTP service are now available.
These services are restored from disk problem.

Services: ddbj Keywords: Maintenance

System is now available

June 02,2014
The DRA search service "DRAsearch" and FTP service are now available. These services are restored from disk problem.
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[DRA] System temporarily unavailable

May 29,2014

At present, the DRA search service "DRAsearch" and FTP service are temporarily unavailable due to disk problem.
Because we are looking into the cause of this system failure, please follow our twitter @DDBJ_topics and wait the announcement of recovery.

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System temporarily unavailable

May 29,2014
At present, the DRA search service "DRAsearch" and FTP service are temporarily unavailable due to disk problem. Because we are looking into the cause of this system failure, please follow our twitter @DDBJ_topics and wait the announcement of recovery.
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Apology for the FTP service down

May 28,2014

FTP service was down from 0:24 to 9:26 on May 28(JST).As of May 28 12:00(JST), FTP service is now available.

DDBJ sincerely apologize for your inconvenience.

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System temporarily unavailable

May 26,2014
From 9:30 to 14:00, Wednesday May 28, DRA, BioProject and BioSample submission and search services will be unavailable due to system maintenance.
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Apology for the DDBJ services down on May 21

May 21,2014

Due to the electric power outage of the NIG(National Institute of Genetics) caused by failure in power transmission at electric power company on May 21, most of DDBJ services were unavailable.

As of 17:00(JST), all DDBJ service is now available.DDBJ sincerely apologize for your inconvenience.

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(Today) DDBJ network service is unavailable

May 21,2014

DDBJ network service is unavailable because of the electric power outage which occurred on May 21.
Please wait for a while till the restoration.

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The 27th International Collaborators Meeting at Mishima

May 20,2014

DDBJ, EMBL-Bank/EBI and GenBank/NCBI hold the International Collaborators Meeting every year to maintain and update international collaboration for nucleotide sequence database construction.

In 2014, the meeting is held at DDBJ in Mishima, May 20-22.

DDBJ will report the decisions at the 27th ICMs on the DDBJ HP that are useful for the data submitters and users of DDBJ.

 ICM photos 2014
  

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New DRA submission system is released

May 13,2014

We have released the new DRA submission system.
For major changes, please see the slides and new handbook.

 DDBJ Sequence Read Archive

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New DRA submission system is released.

May 13,2014

We have released the new DRA submission system. For major changes, please see the slides and new handbook.

(6th, June, 2014)

For submissions with status "new" which had been created before 12th, May, 2014, addition or deletion of metadata objects could cause errors. It is recommended that download metadata as a tab-delimited text file and upload it into a newly created submission.

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For system renewal, the system temporarily unavailable

May 07,2014
From 17:30 May 9th (Fri) until all May 12th (Mon), DRA validation service will be unavailable for the system renewal.
From 9:30 until all May 12th (Mon), DRA, BioProject and BioSample submission and search services will be unavailable as well.
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Release of EST data of domesticated barley (Hordeum vulgare subsp. vulgare)

April 21,2014

DDBJ released EST 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. They are available on getentry.

5' EST: DK584720-DK744249 (159,530 entries)
3' EST: DK744250-DK887267 (143,018 entries)

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Suspension of some parts of DDBJ activities during Japanese holidays

April 18,2014

DDBJ will suspend our business on releasing data and answering inquiries on April 29 and from May 3 to May 6, 2014 due to Japanese national holidays. Search, analysis and other WWW services are available. We will resume the normal business from May 7.

Thank you for your understanding and cooperation.

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BioProject web pages are merged into single Handbook

April 18,2014
The BioProject web pages are merged into single DDBJ BioProject Handbook.
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BioSample web pages are merged into single Handbook

April 18,2014
The BioSample web pages are merged into single DDBJ BioSample Handbook.
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System temporarily unavailable

April 14,2014
From 9:30 to 11:30, Wednesday April 16, DRA, BioProject and BioSample submission and search services will be unavailable due to system maintenance.
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Updated tools related to Mass Submission System (MSS)

April 11,2014

DDBJ updated tools related to Mass Submission System.

  • Utilities for MSS file Error check (UME) V1.34 Released
  • Parser V6.48 Released

See DDBJ Mass Submission in detail.

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getentry, ClustalW web design renewal

April 11,2014

getentry and ClustalW web design renewal.
All other functions remain unchanged.

Please use them.

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Release of microbial genome sequence data related to NBRP and JCM

April 02,2014

DDBJ released microbial genome sequence data related to NBRP and JCM, which had been submitted by University of Tokyo.

Reference
Genome sequencing of JCM strains under the NBRP program.

The accession numbers are as follows. They are available on getentry, DRASearch and BioProject Search, respectively.

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Release of the data related to FANTOM5

April 01,2014

DDBJ released the data related to FANTOM5, which had been submitted by RIKEN.

References
FANTOM5
Forrest A.R.R. et al. (2014) Nature 507: 462-470.
   "A promoter-level mammalian expression atlas"
Andersson,R. et al. (2014) Nature 507: 455–461.
   "An atlas of active enhancers across human cell types and tissues"

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

DRA000991, DRA001101

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New manual DRA Handbook is available

March 27,2014
New manual DRA Handbook is available. This handbook explains how to create a new submission account and submit data to DRA.
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Pages are merged into one page

March 20,2014
DDBJ Trace Archive overview, metadata and submission pages are merged into one page.
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DDBJ Rel. 96.0, DAD Rel. 66.0 Completed

March 18,2014

DDBJ Rel. 96.0

DAD (DDBJ amino acid database) Rel. 66.0
  • Date: Mar. 18, 2014
  • 30,887,377 entries     9,253,624,263 aa (total number of residues)
  • DAD Release Note
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Validation processings are busy

March 18,2014
At present, because large number of files are submitted, the validation system is busy. Submissions with status "data_validating" are in validation process queue, please wait for the validation finishes without stopping the validation.
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Apology for the DDBJ services down on Mar. 13

March 14,2014

Due to the electric power outage of the NIG(National Institute of Genetics) caused by failure in power transmission
at electric power company on March 13, most of DDBJ services were unavailable.

As of March 14, many services work normally.
But some services are still unavailable and we are working to restart them.

Thank you for your understanding and cooperation.

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(Today) DDBJ network services is unavailable

March 13,2014

DDBJ network services is unavailable because of the electric power outage of the NIG(National Institute of Genetics).
Please wait for a while till the restoration.
Thank you for your understanding and cooperation.

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(Mar. 20-25) DDBJ network services and NIG SuperComputer will be unavailable

March 10,2014
NIG SuperComputer and DDBJ network services will be unavailable because of the electric power outage of the NIG(National Institute of Genetics). Schedule is as follows:
[make_table title=yes title_font_weight=bold color="#c9c0bb" set_width=650px]ServicesSchedule (JST)·D-way
·DRA Search
·BioProject Search
·BioSample SearchMarch 20(Thu) 13:00 - March 25(Tue)12:00(JST)·MiGAPMarch 20(Thu) 17:00 - March 25(Tue)10:00(JST)·DDBJ HomePageMarch 20(Thu) 17:00 - March 25(Tue)09:00(JST)·NIG NetworkMarch 21(Fri) 13:00 - Mach 22(Sat) 17:00 (JST)·NIG SuperComputer
·DDBJ HP ·getentry
·ARSA
·DDBJ Nucleotide Sequence Submission System
·BLAST
·ClustalW
·DDBJ Read Annotation PipelineMarch 21(Fri) 13:00 - Mach 24(Mon) 24:00 (JST)[/make_table]


Thank you for your cooperation and understanding.
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System temporarily unavailable

March 06,2014
From 9:30 to 11:30, Wednesday March 12, DRA, BioProject and BioSample submission and search services will be unavailable due to system maintenance.
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System temporarily unavailable due to inspection work

February 28,2014
The submission and search services of DRA, BioProject and BioSample will be unavailable from March 20 (Thu) 13:00 until March 25 (Mon) 12:00 (approx) due to the inspection work of NIG.
(Mar. 20-25) DDBJ network services and NIG SuperComputer will be unavailable
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System temporarily unavailable

February 21,2014
From 9:30 to 10:30, February 26th (Wed), DRA, BioProject and BioSample submission and search services will be unavailable due to system maintenance.
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System temporarily unavailable

February 18,2014
From 9:30 to 10:30, February 19th (Wed), DRA and BioProject submission and search services will be unavailable due to system maintenance.
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DDBJ BioSample starts accepting submissions

February 12,2014
The DDBJ BioSample started accepting new submissions from 12th, February.
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DDBJ BioSample starts accepting submissions

February 12,2014

The DDBJ BioSample started accepting new submissions from February 12. INSDC members have been assigning strain-level taxonomy IDs to microbes whose genomes have been submitted to the INSDC. The INSDC stopped assigning strain-level taxonomy IDs on February 10 and BioSample IDs define microbial genomes instead of strain-level taxonomy IDs.

For details, please refer to the following paper: Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records. Stand. Genomic Sci. 2014 9:3 doi:10.4056/sigs.4851102

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Improvement of DDBJ ARSA

February 10,2014

DDBJ improved DDBJ's keyword retrieval system ARSA(All-round Retrieval and Annotation). Details are as follows.

  • Get the Result
    • All entries are downloaded by "Download ALL" button(Up to 1million)
    • Selected(Checked) entries are available (view on the screen) by "View Selected " button
    • Output format are FlatFile/XML/Fasta.
    (The maximum entries shown on the screen is 100,000. When your result is over it, "Download All", or refine your search)
  • URL changed(Please ovewrite your bokmark)
  • Following search conditions are available
    • Regular expression
    • Phrase including symbols
    • Similar queries with Apache Lucene
  • Version upgrade of search engine (Apache Solr 3 → Apache Solr 4)
DDBJ will continue to improve the services. Your reviews and comments will be helpful for DDBJ's improvement. Please send your comments from "Contact Us" page. (Please select the item "Web Support ")
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Updated tools related to Mass Submission System (MSS)

February 07,2014

DDBJ updated tools related to Mass Submission System.

  • Utilities for MSS file Error check (UME) V1.33 Released
  • Parser V6.47 Released
  • transChecker V2.14 Released

See DDBJ Mass Submission in detail.

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Release of TSA data of Porites australiensis coral

January 30,2014

DDBJ released TSA data derived from Porites australiensis corals, which had been submitted by Okinawa Institute of Science and Technology (OIST).

ReferenceOIST NEWS CENTER

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

    TSA: FX435232-FX505330, FX799345-FX804242 (74,997 entries)
    raw data: DRR003753

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PDB 2014-01-25 released

January 30,2014

PDB 2014-01-25 was released.

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UniProt 2014_01 released

January 30,2014

UniProt 2014_01 was released.

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PDB 2014-01-18 released

January 24,2014

PDB 2014-01-18 was released.

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(Jan.22) DRA/BioProject/BioSample System temporarily unavailable

January 21,2014
Due to system maintenance, some services of DRA/BioProject/BioSample is temporarily unavailable as follows.[make_table set_width=500px title=yes title_font_weight=normal color=#efece5]Serviceunavailable period・D-way
・DRA Search
・BioProject SearchJan. 22(Wed) 9:30~10:30 (JST)[/make_table]
Thank you for your understanding and cooperation.
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System temporarily unavailable

January 21,2014
From 9:30 to 10:30, January 22nd (Wed), DRA and BioProject submission and search services will be unavailable due to system maintenance.
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PDB 2014-01-11 released

January 16,2014

PDB 2014-01-11 was released.

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PDB 2014-01-04 released

January 16,2014

PDB 2014-01-04 was released.

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