Last updated:2014.11.20.

What’s New(2008)

(Urgent)ARSA is unavailable Jan.5, 2009
ARSA is a high-speed data retrieval system provided by DDBJ via WWW and Web API .
Because of the system trouble broken out during the holidays, at present, ARSA is unavailable.
We will announce on this page when they resume.
Thank you for your cooperation.
The service was resumed (at 11:00).

DDBJ Rel. 76 Completed Dec.24, 2008

Release of new mouse hippocampus CAGE MGA 552,486 entries Dec. 16, 2008
DDBJ newly released mouse hippocampus CAGE MGA 552,486 entries,
which had been submitted by RIKEN Omics Science Center.
Accession numbers: AGAAA0000001-AGAAA0552486 (552,486 entries)
Reference site: RIKEN Omics Science Center
Related page: about MGA entry
anonymous FTP:AG_resource_index
These entries were released as DDBJ daily updates on 12/11.

NIG supernig service temporary down Dec. 12, 2008
We are preparing for migration of supernig system to new system.
NIG (National Institute of Genetics) supercomputer (supernig) service will be unavailable during migration.
Date & Time:December 11 (Thu) from 17:00 to 15 (Mon) 9:00
Thank you very much for your understanding and cooperation.

NIG Network service and supernig temporary down Nov. 26, 2008
NIG (National Institute of Genetics) network service will be unavailable at the following schedule,
because of the network maintenance.
All DDBJ network services and NIG supercomputer (supernig) service will also be unavailable.
Date & Time:December 3 (Wed) from 15:00 to 17:00
Thank you very much for your understanding and cooperation.

Release of new genome sequence data of an endosymbiont within protist cells in termite gut, 5 entries Nov. 25, 2008
DDBJ newly released genome sequence data of an endosymbiont within protist cells in termite gut (Candidatus Azobacteroides pseudotrichonymphae genomovar. CFP2), which had been submitted by RIKEN. The data are available by getentry.

The accession numbers are as follows;

  • AP010656-AP010660 (5 entries)
These entries were released as DDBJ daily updates on 11/18.

Related site:

DDBJ mail magazine No. 40 was released Nov. 10, 2008
DDBJ mail magazine No. 40 was released as of Nov. 10, 2008. This site covers information such as latest news and novel services related to DDBJ.
In this issue, it contains "New function is added to ARSA", "Release of sequence data from DDBJ" , "Termination of providing SRS (Sequence Retrieval System) services [Re-announcement]" and etc.
Please read the articles on the site for more details.

New function is added to ARSA Oct.29, 2008
ARSA is a high-speed data retrieval system provided by DDBJ via WWW and Web API . As a functional enhancement of ARSA retrieval system, a new function is added.
It is the function "!" (AND NOT condition) as a logical operator which is used to connect keywords when you specify multiple keyword for a search in Quick search and etc.

The following is a retrieval that you can do by this function.

  • Search: Searching for the entry that contained "lung cancer" but not contained "Homo sapiens" in Quick search.
  • How to enter: Enter the keywords with "!" on the search box like the below.
    "lung cancer"!"Homo sapiens"

    ARSA

  • Result: Displayed the entries that contained "lung cancer", but not contained "Homo sapiens".
It enable us to use "!" (AND NOT conditions) when entering multiple search conditions in a single field.
Please refer to the HELP for more details.

 

DDBJ will do all the more efforts for the development of ARSA. If you have any comments for ARSA, please send it from "Your comment" which is located in the upper blue zone of ARSA.

Exhibit the DDBJ booth in BMB 2008 Oct.28, 2008
BMB 2008 (Joint Annual Meeting of the Molecular Biology Society of Japan and the Japanese Biochemical Society, 2008) is being held at Kobe Port Island from Dec. 9(Tue) to 12(Fri).
DDBJ has the booth in the exhibition that belongs to the event. The posters to introduce the activities and the services of DDBJ are displayed and some information paper is distributed there.

Update of databases related to the H-Invitational Oct.24, 2008
The mirror H-Invitational Database (H-InvDB) was upgraded on
October 23, 2008. The latest version 5.3 of H-InvDB is now
available.

NIG and DDBJ Network services temporary down Oct. 20, 2008
NIG (National Institute of Genetics) network services including NIG supercomputer (supernig) will be unavailable at the following schedule because of the electric power cut.

Accordingly, DDBJ network services will also be unavailable. Please note that the suspended period depends on the service.

Date & Time:From Oct.31 (Fri) 13:00 to Nov.4 (Tue) 17:00 (JST)

DDBJ services suspension schedule:

All services are resumed (at 17:00 Nov.4).

Services Suspend Resume (scheduled)
SAKURA Oct.31 (Fri) 13:00 Nov.4 (Tue) 12:00
getentry, ARSA, SRS,
Homology Search System,
ClustalW, SQmatch,
TXSearch,
Vector Screening System,
PDB Retriever, LIBRA-I,
Lib score,
Oct.31 (Fri) 15:00 Nov.4 (Tue) 12:00
Mirroring H-Inv DB Oct.31 (Fri) 17:00 Nov.4 (Tue) 12:00
GIB Oct. 31 (Fri) 15:00 Nov.4 (Tue) 17:00
Anonymous-FTP Oct. 31 (Fri) 17:00 Nov.4 (Tue) 12:00
DDBJ HP Oct.31 (Fri) 17:00 Nov.2 (Sun) 14:00
NIG supercomputer (supernig) Oct.31 (Fri) 17:00 Nov.4 (Tue) 9:00
Thank you for your cooperation and understanding.

Exhibit the DDBJ booth in BioJapan 2008 Oct.17, 2008
BioJapan 2008 is held at Pacifico Yokohama from Oct. 15 to 17.
DDBJ has the booth in the exhibition. The poster to introduce the activities and the services of DDBJ are exhibited and some information paper is distributed there.

DAD rel. 45.0 was released Oct.16, 2008
DDBJ amino acid database (DAD) Rel.45.0 was released on Oct. 14, 2008 at DDBJ. DAD Rel 45.0 consists of 13,052,722 entries, and the total number of residues reached 3,443,700,325.

The periodical release and the new data are available by FTP download from the "FTP/Web API" page.

ARSA database search (DDBJ, DAD) temporary unavailable Oct. 16, 2008
ARSA is a high-speed data retrieval system provided by DDBJ via WWW and Web API. DDBJ and DAD database search in ARSA is enavailable in the following schedule for update each of released data. TSA division (Transcriptome Shotgun Assemblies) will be provided after this work. Details are as follows:
  • Date & Time: Oct. 22, 2008 (Wed) 9:00 - 18:00 (We will announce on this page when it resumes.)
  • Suspended services:
    • DDBJ and DAD search in ARSA
    • Function of reference in ARSA from TXsearch
    • Search for DNA on DDBJ HP (upper search box)
  • Note: During the above period, ARSA is still available except for the above 2 databases search and also other our service are available.
Thank you for your understanding and cooperation.

Maintenance works finished. Thank you for your cooperation.(Oct. 22, 2008 at 18:00)

Release of new Physcomitrella patens subsp. patens EST 56,525 entries Oct. 3, 2008
DDBJ newly released Physcomitrella patens subsp. patens EST 56,525 entries, which had been submitted by National Institute of Genetics .

The accession numbers are as follows;

  • DC901515-DC958039 (56,525 entries)
These entries were released as DDBJ daily updates on Oct. 1.

FTP site for DB download : Physcomitrella_patens_subsp._patens_EST_081001_1.seq.gz

Related site:

DDBJ Rel. 75 Completed Sep.26, 2008
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public. We completed DDBJ Release 75 on Sep. 25, 2008. DDBJ Release 75 consists of 92,840,037 entries, and the number of bases reached 95,219,505,205.
TSA division (Transcriptome Shotgun Assemblies) started from this release.See the DDBJ release note and The Report for the 21st International Collaborators Meeting for more details.

The periodical release and the new data are available by FTP download from the "FTP/Web API" page.

Some of DDBJ services temporary down caused by network system failure. Sep 26, 2008
Homology search services and ClustalW are temporary down because of the network system failure. Details are as follows.

  • Period: Sep. 26 at 1:20 or later
  • Suspended service: FASTA, BLAST, PSI-BLAST, SSEARCH, HMMPFAM, ClustalW
Recovery work takes little longer.We will announce on this page as soon as the maintenance are completed.

We sincerely apologize for your inconvenience.

The maintenance are completed.All services works normally.(Sep. 26 at 11:00)

DDBJ mail magazine No. 39 was released Sep. 5, 2008
DDBJ mail magazine No. 39 was released as of Sep. 4, 2008. This site covers information such as latest news and novel services related to DDBJ.
In this issue, it contains "DDBJ starts accepting Trace Archive data", "The Report for the 21st International Collaborators Meeting" , "Termination of a part of DDBJ services" and etc.
Please read the articles on the site for more details.

NIG network service temporary down due to electric power failure. Aug. 22, 2008
NIG network service affected by the electric power failure because of lightning that occured on Aug. 21. Details are as follows:

    Date: Aug. 21 (Thu) 18:15

    Affectd service: NIG network service

    Period when all services stopped : Aug. 21 (Thu) 18:15 to 22:30

   &nbspFollowing services are still unavailable:

  • FASTA, BLAST, PSI-BLAST, SSEARCH, HMMPFAM, CLUSTALW
  • ARSA database search for DAD

Recovery work takes a little longer. We will provide an announcement on this page. Thank you very much for your understanding and cooperation.

FASTA, BLAST, PSI-BLAST, SSEARCH, HMMPFAM and ClustalW are resumed. (Aug. 22 at 10:30).

DAD search of ARSA was resumed at 20:00 on Aug.22, and at present, the all service works normally. Sorry for your inconvenience ( Aug. 22 at 20:00).

DDBJ starts providing Trace Archive data constructing it as a part of the integrated database project by FTP. Aug. 19, 2008
DDBJ has accepted Trace Archive data. Trace Archive data which was submitted to DDBJ is now available by FTP from FTP/Web API page.

These data are now available.

supernig suspended for the urgent maintenance Jul. 14, 2008
The access to supernig ( NIG supercomputer system ) from outside of NIG is unavailable,
due to the emergency maintenance of nsclogin. We will provide an announcement on this page as soon as the maintenance are completed.

Date: From 11:45 on July. 14 ( Mon ), 2008

Thank you very much for your understanding and cooperation.

The Maintenance works were completed, and the access from outside of NIG is available now. We apology for the delay of the resume. (July 25 at 12:00)

ARSA database search (DDBJ, DAD) temporary unavailable Jul. 9, 2008
ARSA ( All-round Retrieval of Sequence and Annotation ) is a high-speed data retrieval system provided by DDBJ via WWW. DDBJ and DAD search in ARSA is unavailable in the following schedule for update each of released data. Details are as follows:
  • Date : July 18, 2008 ( Fri ) 9:00 - 18:00 ( We will announce on this page when it resume.)
  • Suspended services:
    • DDBJ and DAD search in ARSA
    • Relational search from TXsearch results
    • DNA search from the window of DDBJ HP
  • Note: During the time, ARSA is available except the above 2 databases . Search results doesn't include those 2 databases.
Thank you for your understanding and cooperation.

Maintenance works finished. Thank you for your cooperation.(July 18, 2008 at 18:00)

DAD rel. 44.0 was released Jul.7, 2008
DDBJ amino acid database (DAD) Rel.44 was released on Jul. 4, 2008 at DDBJ. DAD Rel 44.0 consists of 12,561,319 entries, and the total number of residues reached 3,268,722,437.

The periodical release and the new data are available by FTP download from the "FTP/Web API" page.

Failure in getting result by E-mail in HMMPFAM Jul. 3, 2008
HMMPFAM is the hidden Markov Model based motif search system which is provided by DDBJ via WWW and E-mail servers.
Recently, we found there was uncommonly a problem to provide users with the search result through E-mail server in HMMPFAM.
Details are as follows;


  • Condition : When you specified "E-mail" as Results,
    and the retrieved result was huge, you can't get the reply uncommonly.
  • Cause : Failure in the process which creates the result.
  • Affected period : Feb. 27, 2007 - Jun. 16, 2008
  • Measure : The problem has already been fixed and the service works normally.

We sincerely apologize for your inconvenience.

DDBJ mail magazine No. 38 was released Jun. 30, 2008
DDBJ mail
magazine No. 38
was released. This site covers information about latest news and novel services.

DDBJ Rel. 74 Completed Jun.24, 2008
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public. We completed DDBJ Release 74 on June 24, 2008. DDBJ Release 74 consists of 87,903,140 entries, and the number of bases reached 91,294,770,939.

The periodical release and the new data are available by FTP download from the "FTP/Web API" page.

Apology for the defective results of CON entries in getentry Jun. 20, 2008
getentry is the entry retrieval system by accession numbers etc., which is provided by DDBJ via WWW and E-mail servers.
In the case of sequence display of CON entry, We found there were two problems to display sequences of CON entries.
Datails are as follows;


  • Condition :

    1. When a cited piece entry is described with "complement" operator in a CON entry, the sequence span cited from the piece entry is processed as the forward strand.
      It should be processed into the complementary sequence.   Fixed ( Jul. 3, 2008 )
    2. When the piece entry of retrieved CON entry containes a CON entry, it can not be processed correctly.   Fixed ( Jan. 16, 2009 )

  • Affected parts :
    We have provided two types of methods to get the conjugated sequences of CON entries; display on browser and FTP. However, neither of two methods works properly in the case of retrieving CON entries under the following conditions.

    1. When you specify "total nt seq FASTA" as output format, and "www" , "E-Mail" or "FTP" as Results.
    2. When you specify "Flat file (DDBJ)" as output format, and "www" as Results.
      Then, click each of following links in the result;

      • transfer all the DNA sequences separately in FASTA format
      • display all the DNA sequences separately in FASTA format

      • transfer the combined DNA sequence in FASTA format (Constructed sequence according to CONTIG line)

      • display the combined DNA sequence in FASTA format (constructed sequence according to CONTIG line)

  • Affected services : getentry, ARSA, and Web API (GetEntry)
  • Measure : Recovery work takes a little longer. We will provide an announcement on this page as soon as the problems are solved.

We sincerely apologize for your inconveniece.

Release of new Drosophila EST 190,096 entries Jun. 20, 2008
DDBJ released Drosophila EST 190,096 entries, which had been submitted by Kyoto Institute of Technology.

The accession numbers are as follows;

  • Drosophila auraria 5'-EST : DK265854-DK284650 (18,797 entries)
  • Drosophila auraria 3'-EST : DK284651-DK303963 (19,313 entries)
  • Drosophila sechellia 5'-EST : DK303964-DK322998 (19,035 entries)
  • Drosophila sechellia 3'-EST : DK322999-DK342220 (19,222 entries)
  • Drosophila simulans adult female 5'-EST : DK342221-DK360662 (18,442 entries)
  • Drosophila simulans adult female 3'-EST : DK360663-DK379473 (18,811 entries)
  • Drosophila simulans larvae 5'-EST : DK379474-DK398612 (19,139 entries)
  • Drosophila simulans larvae 3'-EST : DK398613-DK417792 (19,180 entries)
  • Drosophila simulans adult male 5'-EST : DK417793-DK436903 (19,111 entries)
  • Drosophila simulans adult male 3'-EST : DK436904-DK455949 (19,046 entries)
These entries were released as DDBJ daily updates on Jun. 14.

FTP site for DB download : Drosophila_EST_080614_1.seq.gz

Apology for the defect of some search results in getentry Jun. 6, 2008
getentry is the entry retrieval system by accession numbers etc., which is provided by DDBJ via WWW and E-mail servers.
In the case of DAD ( DDBJ Amino Sequence Database ) retrieval with Protein ID in getentry,
there were some search results in which a part of the entry was not displayed properly during the following period.
Datails are as follows;

  • Condition : Displayed unsuitable results under the following conditions.
    When you specify " Protein ID " as " ID ", " DAD ( DDBJ Amino Sequence Database )" as " Database " in getentry,
    there were some entries of setting the CDS Feature with qualifier " /translation " below the CDS Feature with qualifier " /psuedo " in the range of CDS Feature.
    The hyperlink function on the Protein ID in the DDBJ flat file which contained the above " /translation " qualifier doesn't work properly.
    Furthermore, the DAD retrieval with those Protein ID did not display suitable results.

  • Affected Period : Feb. 27, 2007 to May. 22, 2008
  • Accesion numbers at DDBJ entries corresponding with the affected Protein ID : (-> See the list )
  • Measure : The defect has already been fixed and the service works normally.
We kindly request users to conduct their search again if you have used the corresponding entries.

We sincerely apologize for your inconveniece.

BLAST and PSI-BLAST upgraded Jun. 3, 2008
DDBJ provides some homology search services through WWW and E-mail. Among them, BLAST ( by WWW and E-mail ) and PSI-BLAST ( by WWW ) have been upgraded from Ver. 2.2.15 to Ver. 2.2.18.

 

The Blast program provided through NIG supernig server also has been upgraded from Ver. 2.2.15 to Ver. 2.2.18. ( Jun. 11, 2008 )

Release of Lotus japonicus genome data May. 30, 2008
DDBJ released Lotus japonicus genome data, which had been submitted by
Kazusa DNA Research Institute .

The accession numbers are as follows;

These entries were released as DDBJ daily updates on May. 28 and 29.

FTP site for DB download :

Removal of some databases from ARSA May. 22, 2008
ARSA ( All-round Retrieval of Sequence and Annotation ) is the high-speed retrieval system , which is provided by DDBJ via WWW.

Currently, ARSA provides 24 searchable databases including the following 6 PFAM related databases.

  • PFAMA
  • PFAMB
  • PFAMHMMLS
  • PFAMHMMFS
  • SWISSPFAM
  • PFAMSEED

Among them, 4 databases ( PFAMHMMLS, PFAMHMMFS, SWISSPFAM, PFAMSEED )
will be removed from ARSA because of redundant subset of PFAMA as of May 28, 2008.

PFAMA and PFAMB are continuously available.

Thank you very much for your understanding and cooperation.

The removal work was finished. ( May. 28, 2008 at 11:45 )

DDBJ mail magazine No. 37 was released May. 15, 2008
DDBJ mail
magazine No. 37
was released. This site covers information about novel
services and latest news.

Release of new medaka ( Oryzias latipes ) EST 265,853 entries May 7, 2008
DDBJ newly released medaka ( Oryzias latipes ) EST 265,853 entries,
which had been submitted by National Institute for Basic Biology. .

The accession numbers are as follows;

DK000001-DK265853 (265,853 entries)

These entries were released as DDBJ daily updates on May.2.

FTP site for DB download : Oryzias_latipes_EST_080502_1.seq.gz

Apology for the release of the duplicate data in the DDBJ daily update data at the Anonymous FTP May.1, 2008
In the DDBJ daily update release data file at the anonymous FTP. the duplicate data were contained. Deatils are as follows.

  • Corresponding File: DDBJNEWr73.060.CON.gz
  • Accession Numbers:DF090316-DF092116(1801 entries)
  • Measure: the duplicated entries (previously released) was deleted and the corrected files are re-released under the same name.

Anonymous FTP:
At present, the correct data set is available from the FTP site. Therefore, if you had downloaded the corresponding file so far, please download the file again.

We sincerely apologize for your inconvenience.

Release of new silkworm ( Bombyx mori ) genome sequence data Apr.25, 2008
DDBJ newly released silkworm (Bombyx mori) genome sequence data which had been submitted by National Institute of Agrobiological Siences.

The accession numbers and numbers of entreis are as follows;

These entries were released as DDBJ daily updates on Apr. 23 and 24.

FTP site for DB download

Suspension of some parts of DDBJ activities during Japanese holidays Apr.25, 2008
We at DDBJ suspend our business for releasing data and answering all inquires from April 26, 27, 29, and from May 3 to 6, 2008.
Search and analysis and another WWW services are available.
We will resume the normal business from May 7.

Thank you very much for your understanding and cooperation.

ARSA database search (DDBJ, DAD) temporary unavailable Apr. 18, 2008
ARSA is a high-speed data retrieval system provided by DDBJ through WWW. At the following schedule, DDBJ and DAD database search is unavailable for the database update. Details are as follows:
  • Date & Time: April 25, 2008 (Fri) 9:00 - 18:00 (resume will be notified on this DDBJ HP)
  • Suspended services:
    • DDBJ and DAD search in ARSA
    • Function of reference in ARSA from TXsearch
    • Search for DNA on DDBJ HP
  • Note: During the above period, ARSA is still available except for the above 2 databases search and also other our service are available.
Thank you for your understanding and cooperation.

Maintenance works finished. Thank you for your cooperation.(Apr. 25, 2008 at 17:20)

DAD rel. 43.0 was released Apr.14, 2008
DDBJ amino acid database (DAD) Release43 was released on Apr. 11, 2008 at DDBJ. DAD Release 43.0 consists of 12,103,643 entries, and the total number of residues reached 3,118,002,037.

FTP site for DB download

 

[Apology for mistaking a part of CON data for PLN division on the DDBJ Rel.72 and DAD Rel.43]

SRS services unavailable by the network setting trouble Apr.11, 2008
SRS (Sequence Retrieval System) is the keyword retrieval service provided by DDBJ WWW server. Due to the network setting trouble, the service was unavailable from 20:00 on 9th of April to 10:20 on 11th of April today. SRS has been resumed.

We apology for your inconvenicne.

DDBJ Rel. 73 Completed Mar.27, 2008
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public. We completed DDBJ Release 73 on March 27, 2008/. DDBJ Release 73 consists of 83,167,582 entries, and the number of bases reached 86,099,950,395.

The periodical release and the new data are available by FTP download from the "FTP/Web API" page.

 

[Apology for mistaking a part of CON data for PLN division on the DDBJ Rel.72 and DAD Rel.43]
  • DDBJ Rel.72
    • File name: ddbjcon1.seq.gz, ddbjcon1.insd_xml.gz
    • Accession number: reference(3,514 data)
    • Current status: Correction of DDBJ rel.73 (release on March 27,2008)
  • DAD Rel.42
    • File name: ddbjcon1.DAD.gz
    • Accession number: reference(30,434 data)
    • Current status: Correction of DAD rel.43 (release in the first of Aplil,2008)
We apologize very much for your inconvenience, and appreciate your cooperation and understanding.

Release of new rat GSS 331,272 entries Mar.25, 2008
DDBJ newly released rat (Rattus norvegicus) GSS 331,272 entries, which had been submitted by Kyoto University.

The accession numbers are as follows;

DH508174-DH839445 (331,272 entries)

These entries were released as DDBJ daily updates on 3/25.

Anonymous FTP:Rattus_norvegicus_GSS_080325_1.seq.gz

Release of new human small RNAs, MGA 12,134 entries Mar.25, 2008
DDBJ newly released Homo sapiens small RNAs, MGA 12,134 entries,
which had been submitted by RIKEN Genome Sciences Center.

The accession numbers are as follows;

ADAAA0000001-ADAAA0005988 (5,988 Entries)

ADAAB0000001-ADAAB0006146 (6,146 Entries)

These entries were released as DDBJ daily updates on 3/19.

Anonymous FTP: AD_resource_index

Related URL: about MGA entry

NIG network service temporary down Mar. 21, 2008
NIG (National Institute of Genetics) network service will be unavailable at the following schedule, because of the emergency network maintenance. All DDBJ network services and NIG supercomputer (supernig) service will also be unavailable.

Date & Time : Mar 26 (Wed) from 17:00 to 20:00

Thank you very much for your understanding and cooperation.

Maintenance works was finished, and the services are resumed. Thank you for your cooperation.(March 26, 2008 at 19:50)

Correction of the invalid sequence version number for BA000010 and BA000044 Mar. 10, 2008
On 2008/02/19, BA000010 and BA000044 (CON division entries) were distributed with the invalid sequence version number by our operation mistake.
The correct versions were "BA000010.8" and "BA000044.2" respectively, but they appeared as "BA000010.9" and "BA000044.3".

Details are as follows:

  • Relevant accession numbers: BA000010, BA000044
  • Affected DDBJ services and period:
    - getentry /ARSA: 2008/02/19 - 2008/03/05

    - Anonymous FTP site: ftp://ftp.ddbj.nig.ac.jp/ddbj_database/ddbjnew/contig/

    DDBJNEWr72.086.CON.gz: Including the enties with invalid sequence version number ( BA000010.9, BA000044.3 ).

    DDBJNEWr73.014.CON.gz: Including the fixed enties.
  • Cause: A software problem in the flatfile making process.
  • Current status: We have already fixed and deleted the invalid version entries
    in 2008/03/08 on the getentry and annonymous FTP (Daily update).
We apologize for our mistake very much.
 

 

DDBJ started to release patent DNA data by KIPO Mar. 3, 2008
DDBJ constraucts the International DNA Databases, with EMBL in Europe and GenBank in the USA.

DDBJ, EMBL, and GenBank take the publishable patent DNA data into the INSD,
mediating JPO, EPO and USPTO, respectively. And also from this February 2008,DDBJ started to take into and release patent related DNA data by KoreanIntellectual Property Office (KIPO)

Following DNA and protein data from KIPO was released by DDBJ;

  entry number accession number
DNA 168,562 DI000001-DI168562
PROTEIN 113,555 DI500001-DI613555
TOTAL 282,117  

These entries are searchable by getentry.

Note: DDBJ has been functioning as one of the International Nucleotide Sequence
Database Collaboration, including EBI (European Bioinformatics Institute; responsible
for the EMBL database) in Europe and NCBI (National Center for Biotechnology).
Information; responsible for GenBank database) in the USA as the two other members.

The directory of anonymous FTP was changed Feb. 26, 2008
The directory structure of anonymous FTP was changed.
The old directory "database" was divided to "ddbj_database" (DDBJ origin data)
and "mirror_database" (mirror data of another database).

For details of "ddbj_database", please see README.TXT in this directory.

Old directory (database) is maintained for one month, If you watch
regularlly, please change to new directory.

GIB is unavailable for the urgent maintenance Feb. 26, 2008
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because of the urgent maintenance works, GIB is unavailable now. Resusme will be notified on this DDBJ HP. Thank you for your cooperation.
The service was resumed at 16:22 on Feb. 26. Thank you for you cooperation.

Update of the databases related to the H-Invitational Feb. 1, 2008
The contents of the databases related to the H-Invitational were
updated. The main contents of the update are the following.

  • The number of cDNA (HIT; H-Invitational transcript) entry has changed
    from 175,536 to 187,156.

  • The number of LOCUS (HIX; H-Invitational cluster) entry has changed from
    34,699 to 36,073.

  • The version of our mirror H-Invitational Database (H-InvDB) was upgraded
    from "4.6" to "5.0".

[Databases related to the H-Invitational project]

ARSA database search (DDBJ, DAD) temporary unavailable Jan. 21, 2008
ARSA is a high-speed data retrieval system provided by DDBJ through WWW.
At the following schedule, DDBJ and DAD database search is unavailable for the database update. Details are as follows:

  • Date & Time: January 29, 2008(Tus) 9:00 - 18:00 (resume will be notified on this DDBJ HP)
  • Suspended services:
    • DDBJ and DAD search in ARSA

    • From the TXSearch, link to ARSA
    • From search window item DNA on the DDBJ top page, link to ARSA
  • Note: During the above period, ARSA is still available except for the above 2 databases search.
    If you would like to hasten to the search of the above 2 databases, please substitute SRS.

  • Alteration:In the DDBJ database in the ARSA, amino acid translation in the CDS feature was excluded from the specifiable features from this release72.
    In the ARSA, nucleotide sequense data is also not included in the query values.

Thank you for your understanding and cooperation.
Maintenance works finished. Thank you for your cooperation.(Jan. 29, 2008 at 18:00)

DAD rel. 42.0 was released Jan. 21, 2008
DDBJ amino acid database (DAD) Release 42 was released on 1. 8, 2008 at DDBJ. DAD Release 42.0 consists of 11,715,518 entries,
and the total number of residues reached 2,995,558,433.
FTP site for DB download

[URGENT] Supernig temporary down Jan. 22, 2008
Supernig (NIG supercomputer system) is unavailable today,
because of the emergency network maintenance.
All DDBJ network services and NIG supercomputer (supernig) service will also be unavailable.
Date & Time:January 22 (Tue), 2008 from 15:00 to 16:00 (JST)
Thank you very much for your understanding and cooperation.
Maintenance works finished, and the services are resumed. Thank you for your cooperation.(21:00)

Report for DDBJ activicies in NAR Jan. 16, 2008
The new and significant DDBJ activities of the year 2007 were introduced in the following paper appeared in Nucleic Acids Research Vol.36 Database Issue (Jan, 2008 ).

"DDBJ with new system and face"
H. Sugawara, O. Ogasawara, K. Okubo, T. Gojobori and Y. Tateno
Nucleic Acids Research, 2008, Vol. 36, Database issue D22-D24
(Summary) DDBJ activitiew of 2007 (Data submissions and release, New Computer System, ARSA(New keyword search system) enhancement, etc).

NIG and DDBJ network services temporary down Jan. 11, 2008
NIG (National Institute of Genetics) network service will be unavailable at the following schedule because of the SuperSINET maintenance.
DDBJ network service and NIG supercomputer (supernig) service will also be unavailable.

  • Date:January 16(W), 2008 at 12:00 - 13:00 JST
    10 minutes interception during the above time

Thank you very much for your understanding and cooperation.

DDBJ Rel. 72 CompletedDec. 25, 2007
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public. We completed DDBJ Release 72 in December 25, 2007. DDBJ Release 72 consists of 79,004,098 entries, and the number of bases reached 82,592,245,487.
The periodical release and the new data are available by FTP download from the "FTP/Web API" page.
As was already notified, DDBJ proceeded deletion of the both phone and fax numbers, and E-mail address from the flat files of the entries submitted to DDBJ. The retrofit of the all entries was completed by the issue of this release 72. Hereafter, database users become difficult to contact submitters based on the information described in the DDBJ flat files. When you wish to contact to the submitter(s) of an entry of your interest, please contact us using the prescribed inquiry form placed in the DDBJ HP.
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