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What's New (2010)

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Release of genome sequence of an uncultivated thermophilic archaeon Dec. 28, 2010
DDBJ released genome sequence of an uncultivated thermophilic archaeon (Candidatus Caldiarchaeum subterraneum), which had been submitted by the Japan Agency for Marine-Earth Science and Technology.

Reference URL: http://www.jamstec.go.jp/e/about/press_release/20101216/

The accession numbers (file name for Anonymous FTP download) are as follows;
·AB201309 ·AP011633
·AP011650
·AP011675
·AP011689
·AP011708
·AP011733
·AP011724
·AP011727
·AP011745
·AP011751
·AP011786
·AP011796
·AP011826 - AP011902

DDBJ Rel. 84 Completed Dec. 22, 2010

DDBJ will terminate accepting submission by 'Sequin' Dec. 20, 2010
DDBJ has accepted nucleotide sequence data submissions by SAKURA, MSS(Mass Submission System), or 'Sequin'. However, DDBJ will terminate accepting submission by 'Sequin' as of the end of January, 2011. Alternatively, by using SAKURA or MSS, you can submit your data easily and quickly by far. Please use SAKURA or MSS hereafter.
Please use SAKURA or Mass Submission System (MSS) for your future submission to DDBJ.
Reference: Workflow of the data submission to DDBJ
(A) SAKURA
(B) Mass Submission System (MSS)
If you need 'Sequin' submission by unavoidable reason, please send your data to GenBank.
Reference: http://www.ncbi.nlm.nih.gov/Sequin/

Thank you very much for your understanding and cooperation.

DDBJ Sequence Read Archive has released the data search system Nov. 25, 2010
DDBJ Sequence Read Archive has released the data search system (beta). You can search all public data of the DDBJ/EBI/NCBI Sequence Read Archive by accession number, organism name, submitting center name, sequencing platform and study type. Keyword search will be implemented. Metadata is available in XML file and sequencing data can be downloaded in fastq file format. Please try our search system and send us your feedback. For DDBJ/EMBL-Bank/GenBank data, please use getentry and ARSA.

DDBJ Sequence Read Archive is a public repository for next-generation sequencing data at primary analysis phase.


DDBJ network services is unavailable for power outage Nov. 11, 2010
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.
Services Scheduled (JST)
SAKURA Dec.17(Fri) 13:00 - Dec.20(Mon) 12:00 (resumed)
getentry, ARSA, BLAST, ClustalW,
TXSearch, Vector Screening System,
GIB, Anonymous-FTP
Dec.17(Fri) 15:00 - Dec.20(Mon) 12:00 (resumed)
NIG supercomputer (supernig) Dec.17(Fri) 15:00 - Dec.20(Mon) 9:00 (resumed)
DDBJ HP Dec.17(Fri) 17:00 - Dec.19(Sun) 18:00 (resumed)
Thank you for your cooperation and understanding.
All services were resumed. Thank you for your cooperation. (Dec. 20 at 12:00 JST)


RefSeq databases were added in BLAST(WebAPI) Nov. 2, 2010
Following RefSeq databases were added in BLAST(WebAPI) service. Details are Web API services.
  • Reference genomic sequences
  • Reference mRNA sequences
  • Reference protein sequences

Input method of organism names on SAKURA changed Nov. 1, 2010
SAKURA is a nucleotide sequence data submission system through the WWW server at DDBJ.
"Organism Information" page improved. SAKURA organism names input method changed from Oct. 26, 2010. Details are Sequence data submission via SAKURA. And, about the actual input method, please see SAKURA's help page which is shown after you start the submission.

First Japanese whole genome sequencing data are released from the DDBJ Sequence Read Archive Oct. 28, 2010
Center for Genomic Medicine, RIKEN analyzed the whole genome sequence of a Japanese male which had been genotyped by the International HapMap project. As a result, the research group identified over 3 million single nucleotide variations (SNVs), 5,319 deletions smaller than 10 kb as well as 3 million base pairs of novel genome sequences not found in the human reference genome (Press release from RIKEN).

DDBJ Sequence Read Archive has released the sequencing data of the Illumina Genome Analyzer II used in this analysis under the accession number DRA000222.

Trace data determined by "Human full-length cDNA sequencing projects" are available Oct. 20, 2010
A total of 2,445,650 traces determined by the New Energy and Industrial Technology Development Organization (NEDO) "Human full-length cDNA sequencing projects" used to construct the human full-length cDNA clones are available.
These data are available at *DDBJ Trace Archive and NCBI Trace Archive.

  TI numbers:
    ∙ 2282248605-2282527996
    ∙ 2282791904-2284232295
    ∙ 2284242226-2284960269
    ∙ 2284238627-2284240689
    ∙ 2285528775-2285534533

  Anonymous FTP:
    ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dta/FLJ/

*: DDBJ Trace Archive (DTA) is a permanent repository of DNA sequence chromatograms (traces), base calls, and quality estimates for single-pass reads from various large-scale sequencing projects.

Request for the re-submit of the BLAST Oct. 15, 2010
DDBJ asks the users who has executed the BLAST search during the following period to submit again, because the search results returned during might be incorrect. The details are as follows :

  • Period: from Oct. 7, 2010 at 19:00 to Oct. 15, 2010 at 12:30 (JST)
  • Database selection: "16S rRNA"

At present, the BLAST works normally. We apologize for your inconvenience.

Release of new kale (Brassica oleracea var. acephala ) EST 119,204 entries Oct. 13, 2010
DDBJ newly released 119,204 entries of EST data derived from kale (Brassica oleracea var. acephala ) , which had been submitted by Kirin Holdings Company, Ltd.

The accession numbers  (Anonymous FTP)  are as follows ;

These entries were released as DDBJ daily updates on October 13, 2010.

ARSA database search temporary unavailable Oct. 12, 2010
ARSA is a high-speed data retrieval system provided by DDBJ via WWW and Web API . All database search in ARSA is unavailable in the following schedule for the maintenance. Details are as follows:

Date & Time: Oct. 28, 2010 9:00 - 20:00 (JST)
  (We will announce on this page when the service resumes)

Thank you for your understanding and cooperation.
Maintenance works finished. Thank you for your cooperation. (Oct. 28, 2010 at 16:50 JST)


Apologies for the trouble of FASTA file in DAD release Sep. 29, 2010
In DAD release (DDBJ amino acid database), FASTA file had a part of trouble during the following period. Details are as follows:

Corresponding releases: DAD release 10, 18 to 52
Situation:
- An amino residue length over the following size was not correctly displayed in the FASTA format.
    DAD release 10: 7,000 residues or more.
    DAD release 18 to 52: 30,000 residues or more.
- When an amino residue length was over the above size, correct number was not output to the comment line.
    mistake: CP000108-608|ABB27887.1|30030|Chlorobium
    right: CP000108-608|ABB27887.1|36805|Chlorobium
Services: Anonymous FTP(DAD), supernig
Measure: Correct data was released in DAD release 53

We apologize for your inconvenience.

DAD (DDBJ amino acid database) Rel. 53.0 Released Sep. 29, 2010

GIB (Genome Information Broker) temporary down Sep. 28, 2010
GIB (Genome Information Broker) is DDBJ's web service for an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. The service will be unavailable at the following schedule because of the maintenance works.
  • Date: Sep. 29(Wed), 2010 at 15:00 - 17:00 (JST)
Thank you for your cooperation.
Maintenance works finished. Thank you for your cooperation. (Sep. 29, 2010 at 17:10 JST)

(Urgent!) GIB temporary down Sep. 27, 2010
DDBJ's GIB(Genome Information Broker) services provided via WWW is currently unavailable. At present, we are doing recovery efforts for the earliest resume. The resume will be notified on this DDBJ HP. Thank you for your understanding and cooperation.
The service was resumed. DDBJ awfully apologize for your inconvenience. (Sep. 27, 2010 at 17:20 JST)

ARSA database search (DDBJ, DAD) temporary unavailable Sep. 21, 2010
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 83.0, DAD Release 53.0)
Details are as follows:
  • Date & Time:
      Sep. 29, 2010 (Wed) 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.
Maintenance works finished. Thank you for your cooperation. (Sep. 29, 2010 at 18:00 JST)

(Urgent!) GIB temporary down Sep. 21, 2010
DDBJ's GIB(Genome Information Broker) services provided via WWW is currently unavailable. At present, we are doing recovery efforts for the earliest resume. The resume will be notified on this DDBJ HP. Thank you for your understanding and cooperation.
The service was resumed. DDBJ awfully apologize for your inconvenience. (Sep. 21, 2010 at 16:10 JST)


DDBJ Rel. 83 Completed Sep. 16, 2010

BLAST upgraded Sep. 2, 2010
BLAST (by WWW) have been upgraded from Ver. 2.2.18 to Ver. 2.2.24.
(WABI is Sep. 3 upgrade.)

The Report for the 23rd International Collaborators Meeting Sep. 2, 2010
International Nucleotide Sequence Database Collaboration (INSDC), consisted of DDBJ, EBI and NCBI, hold the international collaborators meeting every year.

In 2010, the meeting was held at EBI in UK, 19-21 May, to discuss practical matters to maintain and update nucleotide sequence data archives; DDBJ, EMBL-Bank, GenBank, Sequence Read Archive and Trace Archive. As a result of travel disruptions relating to the Icelandic volcano, the meeting was shorter than expected. Despite these difficulties, we believe that we made significant progress at the meeting. The outcomes of the meeting are summarized here.

Request for the re-submit of the BLAST Sep. 2, 2010
DDBJ asks the users who has executed the BLAST search during the following period to submit again, because the search results returned during might be incorrect. The details are as follows :
  • Period: from Aug. 17, 2010 at 9:00 to Aug. 27, 2010 at 13:00 (JST)
  • Database selection: "16S rRNA"

At present, the BLAST works normally. We apologize for your inconvenience.

"Patent" was added to the BLAST protein search Aug. 27, 2010
DDBJ added patent data to the protein data base of BLAST on August 24, 2010. Japan Patent Office (JPO), Korean Intellectual Property Office (KIPO), United States Patent and Trademark office (USPTO) and European Patent Office (EPO) can be selected. The update is scheduled about four times a year.

patent

The NCBI RefSeq data was released in the mirror Aug. 23, 2010
DDBJ has started to mirror the NCBI RefSeq data from August 23, 2010.
You can download the RefSeq data from DDBJ's Anonymous-FTP site (ftp://ftp.ddbj.nig.ac.jp/mirror_database/refseq/release/).
The directory hierarchy under "/release" is the same as that of NCBI.. The update is scheduled about twice times a month.

NIG supercomputer (supernig) services temporary down Aug. 2, 2010
NIG supercomputer (supernig) service will be stopped as following schedule for system maintenance.

Date: Aug. 10, 2010 at 9:00 - Aug. 11 at 20:00 (JST)
(can not access Supernig system above date)
Thank you for your cooperation.

Release of new fission yeast GSS 113,551 entries and EST 101,079 entries Jul. 28, 2010
DDBJ newly released GSS: 113,551 entries and EST: 101,079 entries derived from fission yeast (Schizosaccharomyces pombe ), which had been submitted by Osaka City University.
koubo
The accession numbers  (Anonymous FTP)  are as follows ;

These entries were released as DDBJ daily updates on Jul. 28, 2010.
(Photo: Integrated Database Project)

"DDBJ Sequence Read Archive" new name Jul. 16, 2010
DDBJ/EBI/NCBI collaboratively archive raw sequencing data from next-generation sequencers. We have decided to call this international activity as "Sequence Read Archive". According to this, we have changed our database name from "DDBJ Read Archive" to "DDBJ Sequence Read Archive".


DAD (DDBJ amino acid database) Rel. 52.0 Released Jul. 13, 2010

Future DAD release schedules
  • DDBJ will make up its periodical release 53 in September 2010 as usual. Though we had informed "DAD periodical release 53 would be prepared in December 2010" in the previous release note, we reconsidered to take back the schedule of DAD periodical releases. We apologize for the confusion.

ARSA database search (DDBJ, DAD) temporary unavailable Jul. 9, 2010
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 82.0, DAD Release 52.0 will be released on July 13, 2010.) Details are as follows:
  • Date & Time:
      Jul. 16, 2010 (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.
Maintenance works finished. Thank you for your cooperation. (Jul. 16, 2010 at 17:30)

DRA has started to distribute public data of DRA/ERA/SRA Jul. 7, 2010
DDBJ Read Archive (DRA) collects and distributes raw output data from next-generation sequencers with NCBI Sequence Read Archive and EBI Sequence Read Archive.
You can download the metadata XML and fastq files released from DRA/ERA/SRA at DRA Download (FASTQ) site.

Request for the re-submit of the BLAST Jun. 30, 2010
DDBJ asks the users who has executed the BLAST search during the following period to submit again, because the search results returned during the period might be incorrect. The details are as follows :
  • Period: from June 22, 2010 at 20:00 to June 23, 2010 at 16:30 (JST)
  • Database selection: "DDBJ ALL (DDBJ periodical release + daily updates)"
  • Cause: error in the data update works

At present, the BLAST works normally. We apologize for your inconvenience.

DDBJ Rel. 82 Completed Jun. 28, 2010

Future DDBJ release schedule
  • DDBJ will make up its periodical release 83 in September 2010 as usual. Though we had informed "DDBJ periodical release 83 would be prepared in December 2010" in the previous release note, we reconsidered to take back the schedule of DDBJ periodical releases. We apologize for the confusion.


Release of new mouse (Mus musculus ) embryo small RNAs, MGA 397,593 entries Jun. 15, 2010
DDBJ newly released small RNA sequences, 397,593 entries of MGA data derived from mouse (Mus musculus) embryos, which had been submitted by National Institute of Neuroscience.

The accession numbers are as follows:
  • ALAAA0000001-ALAAA0130942 (130,942 entries)
  • ALAAB0000001-ALAAB0116883 (116,883 entries)
  • ALAAC0000001-ALAAC0092019 (92,019 entries)
  • ALAAD0000001-ALAAD0057749 (57,749 entries)
Anonymous FTP: AL_resource_index.html

These entries were released as DDBJ daily updates on Jun. 15, 2010.


Started Twitter May 14, 2010
DDBJ started "Twitter". We mainly twitter, about hot topics and updated information etc. http://twitter.com/DDBJ_topics

DDBJ/EMBL/GenBank Feature Table Definition revised May 14, 2010
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 April 2010. Version is 8.3.

Suspension of some parts of DDBJ activities during Japanese holidays Apr. 21, 2010
We at DDBJ suspend our business for releasing data and answering all inquiries on April 29, and from May 1 to 5, 8 and 9, 2010. Search and analysis and another WWW services are available. We will resume the normal business from May 10.
Thank you for your understanding and cooperation.

The Chinese Academy of Science professors visited DDBJ Apr. 16, 2010
chinese academy (April 14, 2010) Six professors of The Chinese Academy of Science (CAS) (include Vice President of CAS) visited NIG and CIB-DDBJ Center. And they held a meeting with CIB-DDBJ staff.

ARSA database search (DDBJ, DAD) temporary unavailable Apr. 14, 2010
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 for update each of released data (DDBJ Release 81.0, DAD Release 51.0). Details are as follows:
  • Date & Time:
      Apr. 23, 2010 (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.
Maintenance works finished. Thank you for your cooperation. (Apr. 23, 2010 at 16:30)


DAD (DDBJ amino acid database) Rel. 51.0 Released Apr. 12, 2009
  • Date: Apr. 9, 2010
  • 16,673,634 entries    4,623,895,321aa (total number of residues)
  • DAD Release Note
  • DAD release continues to include TPA category data, whereas DDBJ periodical release has separated them.
  • Latest Release Information

Future DAD release schedules
  • In accordance with postponement of DDBJ Rel. 83.0 for 3 months, DAD release will be delayed at the same schedule. Therefore, DAD Rel. 53 will also be released in January 2011.

Apologies NIG and DDBJ network inaccessible Apr. 12, 2010
NIG and DDBJ network access was not able to be accessed on Apr. 9. Details are as follows:
  • Period: Apr. 9, 2010 around 9:55 - 13:30(JST)
At present, network is normal. We apologize for your inconvenience.

Release of new Koshihikari rice (Oryza sativa Japonica Group, cultivar Koshihikari ) WGS 654,543 entries Apr. 5, 2010
DDBJ newly released 654,543 entries of WGS data and others derived from Koshihikari rice (Oryza sativa Japonica Group, cultivar Koshihikari ), which had been submitted by National Institute of Agrobiological Sciences.

The accession numbers  (Anonymous FTP)  are as follows;
Reference sites

Release of new purple witchweed (Striga hermonthica ) EST 67,814 entries Apr. 5, 2010
DDBJ newly released 67,814 entries of EST data derived from purple witchweed (Striga hermonthica ), which had been submitted by RIKEN.

The accession numbers  (Anonymous FTP)  are as follows;
Reference URL: Cultivating Tomorrow

These entries were released as DDBJ daily updates on Apr. 2, 2010.

Apology for the trouble of results view in Homology Search Result Retriever Apr. 2, 2010
The Result Retrieiver is a tool for the confirmation of DDBJ's homology search results when you specify "E-mail" as a method for getting the results. In this Result Retriever, a trouble had broken out during the following period. Details are as follows:

  • Period: April 1, 2010 at 9:30 - April 2, 2010 at 12:00 (JST)
  • Situation: The results had not been displayed in the Result Retriever during the above period.
  • Cause: An effect by the works for the termination of some homology search services.
DDBJ deeply apologize for you inconvenience.

Release of new mouse (Mus musculus domesticus ) GSS 122,131 entries Apr. 1, 2010
DDBJ newly released 122,131 entries of GSS data derived from mouse (Mus musculus domesticus ) strain: C57BL/6NCrlCrlj, which had been submitted by RIKEN BioResource Center.
mouse
The accession numbers  (Anonymous FTP)  are as follows ;
Reference URL: DNA BANK

These entries were released as DDBJ daily updates on Apr. 1, 2010.
(Photo: Integrated Database Project)

Change of UniProt release numbers and release cycle Mar. 31, 2010
DDBJ provides the UniProt database (UniProt, UniProt/Swiss-Prot, UniProt/TrEMBL) by Anonymous FTP download, and through getentry, ARSA, FASTA/BLAST search services. The data are updated periodically according to the UniProt's updates.
From the issue of March 23, 2010, UniProt changed the release cycle and release numbers. The details are as follows. Please note that the same numbering scheme was applied to Swiss-Prot and TrEMBL release numbers.

          release number format release cycle                            
       current: YYYY_XX 4weeks
       past: x.n 3weeks

where YYYY is the calendar year and XX is a 2-digit number that is incremented for each release of a given year,
e.g. 2010_01, 2010_02, etc.

Please refer:

DDBJ Rel. 81 Completed Mar. 26, 2010

Future DDBJ release schedules

Removal of "KEGG PATHWAY" from ARSA Mar. 16, 2010
DDBJ will remove "KEGG PATHWAY" from searchable databases in ARSA, as of March 31, 2010. DDBJ apologize for your inconvenience, and thank you for your cooperation.

Release of new tomato (Solanum lycopersicum) GSS 93,682 entries Mar. 3, 2010
DDBJ newly released 93,682 entries of GSS data derived from tomato (Solanum lycopersicum), cultivar: Micro-Tom, which had been submitted by University of Tsukuba.
tomato
The accession numbers  (Anonymous FTP)  are as follows ;

These entries were released as DDBJ daily updates on Mar. 3, 2010.
(Photo: Integrated Database Project)

JPO and KIPO amino acid sequence data are available by Anonymous FTP Feb. 26, 2010
DDBJ start to distribute amino acid patent data of Japan Patent Office (JPO) and Korean Intellectual Property Office (KIPO), by anonymous FTP from Feb. 26.
For more information, please refer README.TXT about the patent data on Anonymous FTP, README.TXT on ddbj_database, and What's New (Feb. 19).

NIG and DDBJ network services temporary down Feb. 25, 2010
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. 21(Sun), 2010 at 18:15 - 19:00 (JST)
    5 minutes interception during the above time
Thank you for your cooperation.

JPO and KIPO amino acid sequence data are available by Anonymous FTP Feb. 19, 2010
DDBJ starts to distribute amino acid patent data of Japan Patent Office(JPO) and Korean Intellectual Property Office (KIPO), by anonymous FTP, from February 26, 2010. These amino acid patent data has already been released from DDBJ, since 2008. At the FTP site, JPO and KIPO data construct each files/directories. The update frequency schedules almost quarterly. In DDBJ, the nucleotide sequence data of JPO and KIPO has already been released as DDBJ release, which also contains EPO and USPTO data.
For more information, please refer README.TXT about the patent data on Anonymous FTP.

NIG and DDBJ network services temporary down Feb. 18, 2010
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.
Service Period
- SAKURA Mar. 12(Fri) 17:00 - Mar. 15(Mon) 10:00(JST)
- DDBJ network services (excluding SAKURA)
- NIG supercomputer (supernig)
Mar. 14(Sun) 9:00 - 21:30(JST)
Thank you for your cooperation.

Release of new mouse (Mus musculus) small RNA MGA 84,606 entries Feb. 17, 2010
DDBJ newly released 84,606 entries of small RNAs, MGA data, derived from mouse (Mus musculus), which had been submitted by Kinki University.

mouse The accession numbers are as follows;
  • ANAAA0000001-ANAAA0033164 (33,164 entries)
  • ANAAB0000001-ANAAB0051442 (51,442 entries)
Anonymous FTP: AN_resource_index
Related site: About Mass sequence Genome for Sequence (MGA) entry

These entries were released as DDBJ daily updates on Feb. 16, 2010.
(Photo: Integrated Database Project)

Homology Search and ClustalW temporary down Feb. 10, 2010
DDBJ's Homology Search and ClustalW services provided via WWW is temporarily unavailable in the following schedule for the system maintenance.

  • Date & Time: Feb. 16, 2010 (Tue.) at 9:00 - 17:00 (JST) (We will announce on this page when it resumes.)
  • Unavailable services:
      - Homology Search (FASTA, BLAST, PSI-BLAST, SSEARCH, HMMPFAM)
      - ClustalW

Thank you for your cooperation.
Maintenance works was finished. Thank you for your cooperation.(Feb. 16, 2010 at 17:00 JST)

Release of new pig (Sus scrofa) EST 82,326 entries Feb. 4, 2010
DDBJ newly released 82,326 entries of EST data derived from pig (Sus scrofa), which had been submitted by National Institute of Agrobiological Sciences.
buta
The accession numbers  (Anonymous FTP)  are as follows ;

These entries were released as DDBJ daily updates on Feb. 4, 2010.
(Photo: Integrated Database Project)


The 9th Japan-Korea-China Bioinformatics Training Course (April, 2010 at Shanghai, China) Feb. 01, 2010
"The 9th Japan-Korea-China Bioinformatics Training Course" will be held at the Shanghai, China, in April 19-23, 2008.
This course is for the graduate school students and postdoctoral fellows, and all lectures and exercises are given in English. If you are interested to participate in this training course as a trainee, see the details in the site , and apply it.

NIG and DDBJ network services temporary down Jan. 20, 2010
NIG (National Institute of Genetics) network service will be unavailable at the following schedule because of the signet router maintenance. DDBJ network service and NIG supercomputer (supernig) service will also be unavailable.

  • Date: Jan. 28(Thu), 2010 at 00:00 - 2:00 (JST)
    15 minutes interception during the above time
Thank you for your cooperation.

ARSA database search (DDBJ, DAD) temporary unavailable Jan. 15, 2010
ARSA is a high-speed data retrieval system provided by DDBJ via WWW and Web API. DDBJ and DAD database search in ARSA is unavailabel in the following schedule for update each of released data (DDBJ Release 80.0, DAD Release 50.0). Details are as follows:
  • Date & Time: Jan. 22, 2010 (Fri) 09:00 - 18:00 (We will announce on this page when the service resumes)
  • Unavailabel services:
      DDBJ and DAD search in ARSA (another 18DBs 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. 22, 2009 at 16:30)

DAD (DDBJ amino acid database) Rel. 50.0 Released Jan. 15, 2009
  • Date: Jan. 14, 2009
  • 16,207,520 entries:    4,480,429,655aa (total number of residues)
  • In the present release, the format of the SOURCE line in DAD flat file has been changed (change of the order of organism name and organelle name, and inclusion of a common name in some of DAD flat files). For details, please refer the DAD Release Note.
  • Latest Release Information

Release of new false killer whale (Pseudorca crassidens) GSS 90,007 entries Jan. 7, 2010
DDBJ newly released 90,007 entries of GSS data derived from false killer whale (Pseudorca crassidens), hich had been submitted by Korea Research Institute of Bioscience and Biotechnology.

The accession numbers  (Anonymous FTP)  are as follows ;
Reference site
These entries were released as DDBJ daily updates on Jan. 7, 2010.

DDBJ/EMBL/GenBank Feature Table Definition revised Jan 4, 2010
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 December 2009, FT-Doc is updated, based on the 22nd International Collaborators Meeting.

Apology for the failure of ClustalW running Dec 28, 2009
DDBJ provides ClustalW via WWW.
During the following period, analysis had not been executed. The details are as follows:
  • Period: Dec 28(Mon), 2009 from 0:00 to 12:00 (JST)
  • Condition: After submitting the queries, although the Request IDs are displayed, the results cannot be views in the screen.
  • Cause: Results which should have been deleted after a elapse of a certain period automatically, cumulated to the system limit. As a result, new analysis was not executed.
  • Measure: Results were removed manually.

At present, the system works normally. If you had submitted queries during the above period and could not view its results, please submit the queries again. We apologize for your inconvenience.

DDBJ Rel. 80 Completed Dec. 25, 2009
  • 112,314,250 entries:    109,636,862,252 bases
  • In the present release, the format of the SOURCE line in DDBJ flat file has been changed ( change of the order of organism name and organelle name, and inclusion of a common name in some of DDBJ flat files). For details, please refer the DDBJ Release Note.
  • Latest Release Information

Report for DDBJ activities in NAR Dec. 25, 2009
DDBJ activities were introduced in the following papers appeared in Nucleic Acids Research Vol.38 Database Issue (Jan.2010).

"DDBJ launches a new archive database with analytical tools for next-generation sequence data"
Kaminuma E, Mashima J, Kodama Y, Gojobori T, Ogasawara O, Okubo K, Takagi T and Nakamura Y.
Nucleic Acids Research, 2010, Vol. 38, Database issue D33-D38

"Archiving next generation sequencing data"
Shumway M, Cochrane G and Sugawara H.
Nucleic Acids Research, 2010, Vol. 38, Database issue D870-D871

Closing H-Inv DB mirror site Dec. 8, 2009
CIB-DDBJ will close H-Invitational Database (H-Inv DB) mirror site as of Dec. 31, 2009. Accordingly, anoymous-FTP will be shifted from the H-InvDB server to the DDBJ server.
"H-InvDB" is an integrated database of human genes and transcripts. CIB-DDBJ and Biomedicinal Information Research Center (BIRC) constructed "H-Inv DB" to inform the result of functional annotation of full-length cDNA data set analyzed by H-Invitational since April, 2004. In addition, DDBJ released functional annotation at "H-Invitational Database CIB-DDBJ Flat File Server", by the flat file format based on an International Nucleotide Sequence Database.
Hereafter, please use BIRC H-InvDB site. Thank you for your access to H-Inv DB mirroring site.