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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 system maintenance. 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)

Termination of a part of DDBJ services Feb. 03, 2010

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.

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