Last updated:2014.12.5.

What’s New(2006)

Release of new Medaka GSS 430,750 entries Dec.27, 2006
DDBJ newly released Medaka (Oryzias latipes, strain Hd-rR) GSS 430,750 entries, which had been submitted by National Institute of Genetics. These entries were released as DDBJ daily updates on Dec. 22, 23 and 26.

Genome data were added to GIB Dec 27 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the following genome sequence data were released from December 19 to 26, we incorporated them to GIB, and now you can search those data.

  • Azoarcus sp. BH72 (by University of Bremen)
  • Thermofilum pendens Hrk 5 (by Joint Genome Institute)
  • Nocardioides sp. JS614 (by Joint Genome Institute)
  • Yersinia enterocolitica subsp. enterocolitica 8081 (by Sanger Institute)
  • Mycobacterium sp. KMS (by Joint Genome Institute)
  • Pyrobaculum islandicum DSM 4184 (by Joint Genome Institute)
  • Shewanella amazonensis SB2B (by Joint Genome Institute)
  • Psychromonas ingrahamii 37 (by Joint Genome Institute)
  • Borrelia turicatae 91E135 (by National Institutes of Allergy and Infectious Disease)

BLAST and PSI-BLAST upgraded 2006.12.26
DDBJ upgraded BLAST (provided through WWW and E-mail) and PSI-BLAST (WWW only), which are DDBJ's homology search services , from 2.2.14 to 2.2.15. The upgraded services corresponds to the retrieval of the amino acid including "J" and "O".

Failure in getting the result by FTP in the WWW getentry Dec. 21, 2006
"getentry" is the entry retrieval system by accession numbers etc, which is provided by DDBJ via WWW and E-mail servers. Recently, we found that getting the result by FTP was temporarily unavailable. Details are as follows:

  • Period: aound Dec. 13, 19:30 - around Dec. 14, 16:05
  • Conditions:
    1. At WWW getentry, the result files for FTP .
    2. At E-mail getentry, the result by FTP were not created under the following conditions:
      • search more than 10 entries
      • specify DATABASE as [DDBJ],
      • specify ID as [Accession],
  • Cause:
    Because an enormously huge size file occupied the whole disk space, no more FTP files were created.

  • Affect:
    If you did the search during the above period specifying FTP for getting the result, FTP files may not have been created. So, plase do the search again. At present, the problem have already been removed.
We deeply apologize for any inconveniences that this may have caused to our users. We will try to set the preventive measures to cope with these troubles immediately.
PRF Rel. 112 was released Dec 19, 2006
PRF (Protein Research Foundation)/SEQ database Release 112 was released on Dec. 18, 2006 at DDBJ. PRF Release 112 consists of 709,985 entries, and the total number of residues reached 242,521,349.
Genome data were added to GIB Dec 19, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the following genome sequence data were released from December 12 to 18, we incorporated them to GIB, and now you can search those data.

  • Chlorobium phaeobacteroides DSM 266 (by Joint Genome Institute)

Correction for the "Release of new Xenopus laevis EST 129,076 entries (Dec.6)" Dec. 18 2006
In the "Release of new Xenopus laevis EST 129,076 entries (Dec.6)", the description of the organism name was corrected in some data. Details are as follows. For the Anonymous FTP, the new file which contains the corrected data was placed on the following site. Please download the files again, and replace with the old ones.
  • Organism name
    (Error) Xenopus laevis  ---> (Correct) Xenopus tropicalis
    DC135518-DC165593 (30076 entries)
    DC165594-DC195410 (29817 entries)
  • Correction for the developmental stage description
    (Error) stage 10.5 --->
    (Correct) mixture of equivalent stages 10.5-15 (early gastrula to mid neurula)
    DC066335-DC099907 (33573 entries)
    DC099908-DC135517 (35610 entries)
  • Anonymous FTP:

    Xenopus tropicalis EST
    (file name) Xenopus_tropicalis_EST_061215_1.seq.gz
      Xenopus_laevis_EST_061215_2.seq.gz
    Xenopus laevis EST
    (file name) Xenopus_laevis_EST_061215_1.seq.gz
      Xenopus_laevis_EST_061215_2.seq.gz

We apologize for your inconvenience.
"16S rRNA" is newly added to DDBJ homology search databases Dec 15, 2006
DDBJ provides homology search services by WWW and E-mail. "16S rRNA" is newly added to the searchable databases in FASTA, BLAST, and SSESRCH services. Deatils are as follows.

  • Database: 16S rRNA (Prokaryotes)
  • method:
    1. The 16S rRNA sequences which meets the following conditions were extracted from BCT division of the latest DDBJ periodical release.
      • include "rRNA" in Feature Key
      • include 16S", "RRS" or "SSU" in the product line of Qulifier Key.
    2. After extraction, the sequences whose length is 300bp or less and which ar recognized as the antisense were removed.
  • Anonymous FTP:
Genome data were added to GIB Dec 14, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the following genome sequence data were released from December 5 to 11, we incorporated them to GIB, and now you can search those data.

  • Pelobacter propionicus DSM 2379 (by Joint Genome Institute)
  • Mycobacterium ulcerans Agy99 (by Institut Pasteur)
  • Candidatus Ruthia magnifica Cm (Calyptogena magnifica) (by Joint Genome Institute)
  • Bifidobacterium adolescentis ATCC 15703 (by Gifu University)

Failure in part of search services in the WWW getentry Dec. 8 2006
"getentry" is the entry retrieval system by accession numbers etc,
which is provided by DDBJ via WWW and E-mail servers.

Recently, we found there were some entries which had not been displayed on the web version of getentry for a certain period (see below for details).

We kindly request users to conduct their searchesagain if you have used the web version of getentry in the affected period. Currently, the web version of getentry works normally.

Fortunately, the e-mail version of getentry was not affected by this trouble.

Details are as follows:

  Period: Dec. 5, 15:00 - Dec. 6, 14:00
  Cause: bug at the web version program for the display of the results
  Condition: Users could not view the results under the following conditions.
      - when you specify:
ID as [Accession],
DATABASE as [Flat File (DDBJ)],
Result as [WWW] and
enter the accession numbers which start from C, CZ, or X
We deeply apologize for any inconveniences that this may have caused to our users.
We will try to set the preventive measures to cope with these troubles immediately.

Release of new Xenopus laevis EST 129,076 entries Dec.6, 2006
DDBJ newly released African clawed frog (Xenopus laevis) EST 129,076 entries, which had been submitted by National Institute for Basic Biology. These entries were released as DDBJ daily updates on Dec. 5.

Reference URL: http://www.shigen.nig.ac.jp/xenopus/top.jsp

The accession numbers and the file names for anonymous FTP are as follows;

  • DC066335-DC195410 (129,076 entries)
  • anonymous FTP: Xenopus_laevis_EST_061205_1.seq.gz

Codon usage table is available at GIB Dec.6, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

The codon usage table was added to GIB. The frequency of the codon use in the chromosomes and in the plasmids is available.

Click on "Codon Usage" from the left menu of the page of each species.
Genome data were added to GIB Dec 6, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the following genome sequence data were released from¡¡November 21 to December 4, we incorporated them to GIB, and now you can search those data.

  • Clostridium novyi NT (by Howard Hughes Medical Institute and Ludwig Center for Cancer Genetics & Therapeutics at the Johns)
  • Mycobacterium avium 104 (by The Institute for Genomic Research)
  • Mycobacterium smegmatis MC2 155 (by The Institute for Genomic Research)
  • Bacillus thuringiensis Al Hakam (by The Joint Genome Institute)
  • Campylobacter fetus subsp. fetus 82-40 (by The Institute for Genomic Research)
  • Francisella tularensis subsp. novicida U112 (by University of Washington)

Release of new Xenopus laevis EST 66,334 entries Dec.5, 2006
DDBJ newly released African clawed frog (Xenopus laevis) EST 66,334 entries, which had been submitted by University of Tokyo. These entries were released as DDBJ daily updates on Dec. 2.

Reference URL: http://www.shigen.nig.ac.jp/xenopus/top.jsp

The accession numbers and the file names for anonymous FTP are as follows;

  • DC000001-DC066334 (66,334 entries)
  • anonymous FTP: Xenopus_laevis_EST_061202_1.seq.gz

NIG Network service temporary down Dec. 4 2006
NIG (National Institute of Genetics) network service will be unavailable at the following schedule, because of the preliminary works of the computer system replacement in NIG with an upgraded one by March, 2007. All DDBJ network services and NIG supercomputer (supernig and minerva2) service will also be unavailable.

Date & Time: Dec.9 (FRI) from 8:00 to 18:00

Thank you very much for your understanding and cooperation.

supernig suspended for the urgent maintenance Dec 4, 2006
Because of the emergency maintenance, supernig service is unavailable now. Thank you very much for your understanding and cooperation.

resumed (Dec.4 17:30)

Suspension of the DDBJ activity during the New Year Holidays Nov 29, 2006
We at DDBJ will temporally close our business for the New Year Holidays in the following schedules, according to the Japanese custom, and resume the normal business on January 4th, 2007.

Please note in particular that SAKURA will also stop in operation for a while (see below). However, the computer search and analysis and FTP are available during the holidays.

DDBJ activity suspension: from December 29th, 2006 to January 3rd, 2007
SAKURA suspension: from December 27th, 2006 to January 4th, 2007
data release suspension: from December 27th, 2006 to January 4th, 2007
 

Thank you very much for your understanding and cooperation.

We wish you a Happy New Year.

GIB temporary suspension for maintenance Nov. 29, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Suspension of the GIB service will be scheduled as follows.

Date & Time: December 4, 2006 (Mon9:00 - 13:00

Affected Services:FASTA and BLAST in GIB

Thank you very much for your understanding and cooperation.

DDBJ services emergency trouble caused by network system failure Nov 22, 2006
Because of the network system failures, connection to some DDBJ services are being
unstable now. Details are as follows.

Date and time: 11:00 on Nov 21- (JST)

Affected services:

  • Database Searches : getentry, SRS,ARSA

  • Homology Searchs : FASTA, BLAST, SSEARCH
  • Data Analysis¡§ClustalW, malign
  • FTP
Resume of the services will be announced on the DDBJ HP.
Thank you very much for your understanding and cooperation.

Nov.21 18:00 Resumed. Thank you.

Resume of the E-mail reception from free emails Nov. 20, 2006
As the delay of mail delivery was recovered. E-mail reception from the following free mails was restarted.

Date:November 20 (Mon) 15:00-

Domains:

yahoo.co.jp, yahoo.com, hotmail.com, livedoor.com,
infoseek.jp, gmail.com, goo.ne.jp
Thank you for your cooperation.
Genome data were added to GIB Nov 20, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the following genome sequence data were released from¡¡November 11 to 20, we incorporated them to GIB, and now you can search those data.

  • Shewanella sp. ANA-3 (by Joint Genome Institute)
  • Magnetococcus sp. MC-1 (by Joint Genome Institute)
  • Acidothermus cellulolyticus 11B (by Joint Genome Institute)
Integrated Database Renewal Nov. 13, 2006
Integrated Database of Genome Network Platform was updated on 13th Nov. 2006.

"PPI Path Search" is now available.
About the detail, please see below.

http://genomenetwork.nig.ac.jp/index_e.html

Important: Temporary halt of databank activities in February 2007 Nov. 15, 2006
The computer system in the National Institute of Genetics will be replaced with an upgraded one by March, 2007.

Consequently, DDBJ will suspend its activity completely for about a week in late February, 2007. The exact dates will be announced on the home page of DDBJ later in December, 2006.

If, in particular, you plan to submit your data to DDBJ and obtain accession numbers in February, 2007, please keep the dates to be announced in mind.

Thank you very much for your understanding and cooperation in advance.
Update of databases related to the H-Invitational Nov 14, 2006
The mirror H-Invitational Database (H-InvDB) was upgraded on October 26, 2006. The latest version 3.6 of H-InvDB is now available.

Release of new MGA 356,693 entries from Medaka (Oryzias latipes) Nov.14, 2006
A large amount of transcript sequence entries which are categorized as MGA (Mass sequence for Genome Annotation) was released. The newly released data were submitted by a research group of the University of Tokyo. They were derived from Oryzias latipes and were produced by 5'SAGE (5'-end serial analysis of gene expression) method. The total number of sequence entries is 356,693.

Accession numbers for entries;

   ACAAA0000001-ACAAA0356693 (356,693 entries)

Reference URL:

   http://5sage.gi.k.u-tokyo.ac.jp

   http://medaka.utgenome.org

anonymous FTP;
   (MGA directory)

  • Master record; ACAAA_master
  • Variable record; ACAAA_variable.gz
  (Project index)
Genome data were added to GIB Nov 14, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the following genome sequence data were released from October 28 to November 10, we incorporated them to GIB, and now you can search those data.

  • Gramella forsetii KT0803 (by Max Planck Institute)
  • Aeromonas hydrophila subsp. hydrophila ATCC 7966 (by The Institute for Genomic Research)

Restriction of the E-mail reception from free emails Nov. 13, 2006
The reception from the following free emails stops temporarily.

Date:November 11 (Sat) 23:00-

Domains:

yahoo.co.jp, yahoo.com, hotmail.com, livedoor.com,
infoseek.jp, gmail.com, goo.ne.jp
E-mail delivery delay still remains. Thank you for your understanding and cooperation.

Resume of E-mail reception with some limitation Nov. 10, 2006
E-mail reception by NIG E-mail servers, which had been suspended because of a massive amount of
SPAM mails since Nov7, are resumed. But, as SPAM mails are continuously flood to NIG E-mail servers,
E-mail delivery delay still remains. Thank you for your understanding and cooperation.

E-mail reception temporary suspended Nov. 7, 2006
As was announced on Nov. 6, NIG E-mail servers are being targeted by a huge amount of SPAM mails. Therefore, at present, reception of all mails from outside NIG is temporarily suspended. Resume will be announced as soon as the trouble is removed. Thank you for your understanding and cooperation.

E-mail delivery delay Nov. 6, 2006
As of November 6, 11:00, in DDBJ, there is a serious delivery delay of E-mails. Therefore, at present, DDBJ can not (or takes a lot of time) receive inquiry from DDBJ users. This is caused by the attack of a large amount of SPAM mails since November 3, 2006 (Fri) 19:00. If you need a quick response from DDBJ, please understand the present situation.

Thank you very much for your understanding and cooperation.

INSD-XML upgraded to ver 1.4 Nov. 8, 2006
DDBJ upgraded the INSD-XML data format version from 1.3 to 1.4, on October 31, 2006. In DDBJ, INSD-XML data are provided at WWW getentry and anonymous FTP.

  1. 1.INSD-XML ver 1.4 is applied on the all data other than MGA at WWW getentry, and is applied on all the data excluding WGS and MGA at anonymous FTP.
    (Because the original notice was incorrect, this article was rectified. We apologize for it.(Dec.7))
  2. 2.Output format of getentry was changed from ver 1.3 to 1.4. When you do the search specifying DNA as the target database and INSD as the output format, the results are outputted in the ver 1.4 format.
  3. 3.At anonymous FTP, both 1.3 and 1.4 format data are available until the distribution of DDBJ release 68 (around the end of this year).
    INSD-XML version 1.3
    DDBJ release data
    DDBJNEW data
  4. DTD
  5. INSD-XML version 1.4
    DDBJ release data
    DDBJNEW data
    DTD
  6. 4.Hierarchy of anonymous FTP site (where XML data are placed) was also reconstructed. DDBJ release and DDBJ new data are subject to this change.
    • DDBJ-XML was moved from xml/ to xml/ddbjxml/
    • INSD-XML was moved from insd/ to xml/insdxml
    • To obtain the latest version INSD-XML data, please visit xml/insixmlcurrent/
xml/  :  DDBJ-XML data allocated*
xml/insd/  :  INSD-XML v1.3 data allocated*
xml/ddbjxml/  :  DDBJ-XML data allocated
xml/insdxml/  : INSD-XML data allocated
xml/insdxml/v1.3/  : INSD-XML v1.3 data allocated*
xml/insdxml/v1.4/  : INSD-XML v1.4 data allocated
xml/insdxml_current/  : INSD-XML latest version data directory

* xml/ , xml/insd/ and xml/insdxml/v1.3/ are deleted after the release of DDBJ release68 (scheduled in the end of December, 2006)

NIG Network service temporary down Nov. 2 2006
NIG (National Institute of Genetics) network service will be unavailable at the following schedule because of the electric power cut. All DDBJ network services and NIG supercomputer (supernig and minerva) service will also be unavailable. Thank you very much for your understanding and cooperation.

All Network Services: From Nov.10 (FRI) 17:00 to Nov.11 (SAT) 23:00 (JST)

SAKURA server:
From Nov.10 (FRI) 15:00 to Nov.13 (MON) 09:00 (JST)
Genome Sequence of Honeybee Nov. 2, 2006
The honeybee genome sequencing consortium made up of 90 institutes reported the genome sequence of the honeybee, Apis melliferaon Nature 443, 931-949 (26 October 2006).
From Japan, RIKEN GSC and others were associated with the consortium.
Honeybee EST entries submitted from RIKEN GSC were distributed from DDBJ (See previous report).
  • Genome assemblies are available from following site.

    version 4.0; scaffolds: CM000054-CM000069, CH876891-CH878241
    version 3.0; contigs: AADG05000001-AADG05018946
    version 2.0; contigs: AADG04000001-AADG04016028
      scaffolds: CM000054-CM000069,
    CH402995-CH404444
    version 1.2 ; contigs: AADG03000001-AADG03022771
      scaffolds: CM000054-CM000069,
    CH236967-CH239577
    version 1.1; contigs: AADG02000001-AADG02030074
    version 1.0; contigs: AADG01000001-AADG01015795
  • Genome browsers are available for viewing the genome assemblies at
    following sites.

    BeeBase; http://racerx00.tamu.edu/bee_resources.html
    NCBI; http://www.ncbi.nlm.nih.gov
    UCSC; http://genome.ucsc.edu
Release of new sea squirt EST 58,309 entries Nov. 2, 2006
DDBJ newly released sea squirt (Halocynthia roretzi) EST 58,309 entries, which had been submitted by National Institute of Genetics .

The accession numbers are as follows;

DB577969-DB636277 (58,309 entries)

These entries were released as DDBJ daily updates on 11/1.

anonymousFTP:
Halocynthia_roretzi_EST_061101_1.seq.gz
The Minimal Genome Sequence, Bacterial Endosymbiont Carsonella Nov. 2, 2006
DDBJ newly released complete genome sequence of Carsonella ruddii which consists of a circular chromosome of 159,662 base pairs. The entry with accession number AP009180 was submitted by RIKEN.

Reference URL (Japanese):
http://www.riken.go.jp/r-world/info/release/press/2006/061013/index.html

Change of the "tomato" scientific name in the EST option in DDBJ homology search Nov.1, 2006
DDBJ provides homology search services by WWW and E-mail. In FASTA, BLAST, and SSESRCH, you can select organisms in the EST division for the effective search (this selection is available only when "DDBJ ALL" or "DDBJ updates" is selected). According to the scieintific name change of the "tomato" (Lycopersicon seculentum -> Solanum lycopersicum), the EST organism option name is also changed in the same manner.

Details are as follows.

Services : FASTA, BLAST, SSEARCH
  before   ->   after
Scientific name : Lycopersicon esculentum   ->   Solanum lycopersicum
EST option (WWW): L.esculentum   ->   S.lycopersicum
EST option (E-mail): est_lesc   ->   est_slyc
Please refer to the corresponding help page in your search.

Supernig emergency maintenance Oct.30, 2006
Because of System down occured around 0:10 of Oct. 28 (Sat) , Supernig service is unavailable for the urgent maintenance. Thank you very much for your understanding and cooperation.

==>resumed. (Oct.30)
Genome data were added to GIB October 30, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the following genome sequence data were released from October 23 to 27, we incorporated them to GIB, and now you can search those data.

  • Leptospira borgpetersenii serovar Hardjo-bovis L550 (by National Animal Disease Center)
  • Leptospira borgpetersenii serovar Hardjo-bovis JB197 (by National Animal Disease Center)
  • Buchnera aphidicola Cc (Cinara cedri) (by University of Valencia)
  • Solibacter usitatus Ellin6076 (by Joint Genome Institute)
  • Arthrobacter sp. FB24 (by Joint Genome Institute)
  • Burkholderia cenocepacia HI2424 (by Joint Genome Institute)
  • Listeria welshimeri serovar 6b SLCC5334 (by Justus-Liebig-University)
Update of "Conference on Information Biology" October. 27, 2006
Following conferences were added to "Conference on Information Biology"

2006

2007

  • Conference in
    Systems Biology, Bioinformatics and Synthetic Biology
    (1/11-13)
  • 21st International Symposium on MicroScale
    Bioseparation (1/14-17)
  • 7th Spanish
    Symposium on Bioinformatics and Computational Biology (1/22-24)
  • Southern African Bioinformatics Workshop (1/28-30)
  • 2007
    AGBT meeting (2/7-10)
  • Genomic Disorders 2007 (3/21-23)
  • RNAi2007: The Expanding Roles of Small RNAs (3/29-30)
  • 9th
    International Conference on Biology and Synchrotron Radiation
    (8/13-17)
  • International Conference on Mathematical Biology 2007
    (9/4-6)

Apology for the delay of reply from DDBJ Oct.23, 2006
Since October 22, 2006 (Sun) 12:03, there happens a serious E-mail delivery delay because of overloading of NIG E-mail server by the attack of a large amount of SPAM mail.

Therefore, at present, DDBJ can not (or takes a lot of time) receive inquiry from DDBJ users sent by E-mail. If you do not receive the reply in spite of you need a quick assistance of DDBJ, please understand the present situation.

Thank you very much for your understanding and cooperation.

The problem was fixed at the midnight of Oct. 23, and E-mails can be delivered normally. We apologize for your inconvenience.
Genome data were added to GIB October 23, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the following genome sequence data were released from October 16 to 20, we incorporated them to GIB, and now you can search those data.

  • Oenococcus oeni PSU-1 (by Joint Genome Institute)
  • Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365 (by Joint Genome Institute)
  • Lactobacillus gasseri ATCC 3332 (by Joint Genome Institute)
  • Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 (by Joint Genome Institute)
  • Lactobacillus brevis ATCC 367 (by Joint Genome Institute)
  • Streptococcus thermophilus LMD-9 (by Joint Genome Institute)
  • Pediococcus pentosaceus ATCC 25745 (by Joint Genome Institute)
  • Lactobacillus casei ATCC 334 (by Joint Genome Institute)
  • Lactococcus lactis subsp. cremoris SK11 (by Joint Genome Institute)
  • Candidatus Carsonella ruddii PV (by Kitasato University)
Statistics [Top 30 organisms according to the total number of nucleotides]
Update Oct. 20, 2006
Top 30 organisms according to the total number of nucleotides (-DDBJ rel.67)
in Breakdown
statistics was updated with releasing DDBJ rel.67.
Zea mays subsp. mays (corn) was newly ranked in Top 30.
Click the organismname to view the graph of change.

Guidance for Nucleotide Sequence Submission updated Oct.20, 2006
According to the decision in the 19th International Collaborators Meeting, Guidance for Nucleotide Sequence Submission has been updated on October 19, 2006.
Illegal values were included in CONTIG lines of part of ultra-contig and chromosome entries derived from Oryzias latipes (Japanese medaka) WGS dataOct. 20, 2006
Part of ultra-contig and chromosome entries, which were constructed by using Oryzias latipes (Japanese medaka) WGS data, contained illegal values at the location of piece entries in CONTIG lines.

  • The accession and version numbers of wrong ultra-contig and chromosome entries were listed below. At present, all the wrong entries were replaced with corrected ones. The version number of the corrected ultra-contig entries is ".4".

    List of accession and version numbers of the wrong ultra-contigs (42 entries)

    DF076134.3, DF076146.3, DF076156.3, DF076165.3, DF076168.3, DF076174.3,
    DF076189.3, DF076197.3, DF076201.3, DF076203.3, DF076205.3, DF076217.3,
    DF076230.3, DF076245.3, DF076247.3, DF076249.3, DF076256.3, DF076258.3,
    DF076269.3, DF076279.3, DF076281.3, DF076285.3, DF076298.3,
    DF076306.3,
    DF076312.3, DF076313.3, DF076318.3, DF076341.3, DF076366.3, DF076379.3,
    DF076386.3, DF076387.3, DF076391.3, DF076408.3, DF076411.3,
    DF076417.3,
    DF076418.3, DF076425.3, DF076430.3, DF076449.3, DF076456.3, DF076457.3

    List of accession and version numbers of the wrong chromosome (20 entries)

    DG000001.1, DG000002.1, DG000003.1, DG000004.1, DG000005.1,
    DG000006.1,
    DG000008.1, DG000009.1, DG000010.1, DG000011.1, DG000012.1, DG000013.1,
    DG000014.1, DG000016.1, DG000018.1, DG000019.1, DG000021.1, DG000022.1,
    DG000023.1, DG000024.1

We have replaced 24 entries of all chromosomes with updated version like below in order to control the chromosome versions uniformly.

previous version   updated version
DG000001.1-DG000024.1 --> DG000001.3-DG000024.3
DG000001.2-DG000024.2 --> DG000001.4-DG000024.4
DG000001.2-DG000024.2 were transferred to DG000001.4-DG000024.4 without any changes except for the date of LOCUS line and version number
The below three files, which were distributed from our anonymous FTP site:
ftp://ftp.ddbj.nig.ac.jp/ddbj_database/mass/Oryzias_latipes_CON/, contain the entries including the illegal CONTIG lines. Please be careful not to use the three files. At present, the three files were removed from the FTP site and replaced with the revised files.

ftp://ftp.ddbj.nig.ac.jp/ddbj_database/mass/Oryzias_latipes_CON/
Oryzias_latipes_CON_060524_1.seq.gz
Oryzias_latipes_CON_060531_1.seq.gz
Oryzias_latipes_CON_060605_1.seq.gz

  • You can see the revised file list by clicking here.

  • In addition, Oryzias_latipes_CON_060615_1.seq.gz that includes DG000001.2-DG000024.2 was replaced with Oryzias_latipes_CON_061018_1.seq.gz that includes DG000001.4-DG000024.4.
We apologize for your inconvenience.
Supernig periodic maintenance Oct. 16, 2006
Supernig service will be unavailable during the following date because
of the periodic maintenance. Thank you very much for your understanding
and cooperation.

Oct. 20th(FRI) from 12:00 to 21:00
Genome data was added to GIB Oct. 13, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the genome sequence data of Escherichia coli APEC O1 (by Iowa State University) and Pseudomonas aeruginosa UCBPP-PA14 (by Massachusetts General Hospital) were released, we incorporated them to GIB, and now you can search those data.

Whole data download by FTP unavailable Oct. 12, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because of the GIB server down occured on October 12 at 9:00, whole download of GIB data from FTP server is unavailable now. On the other hand, you can separately download each data. The recovery will be notified at DDBJ HP as soon as the normal operation is confirmed. Thank you very much for your understanding and cooperation.

Recovered at 9:30 on October 13. Sorry for your inconvenience.
PRF Rel. 111 was released 2006.10.12
PRF (Protein Research Foundation)/SEQ database Release 111 was released on
Oct. 12, 2006 at DDBJ. PRF Release 111 consists of 656,550 entries,
and the total number of residues reached 225,708,852.

Some GIB data are unavailable Oct. 10, 2006
GIB (Genome Information Broker) provides an integrated
search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because of the GIB server partially down occured on October 7 at 23:00, some GIB data are unavailable now. The recovery will be notified at DDBJ HP as soon as the normal operation is confirmed. Thank you very much for your understanding and cooperation. ¡¡

recovered at 12:00 on October 11. Sorry for your inconvenience.
Genome data was added to GIB Oct. 06, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the genome sequence data of Rhodopseudomonas palustris BisA53 (by Joint Genome Institute) was released, we incorporated them to GIB, and now you can search those data.
DAD rel. 37 was released Oct 04, 2006
DDBJ amino acid database (DAD) Release37 was released on Oct. 04, 2006 at DDBJ. DAD Release 37 consists of 3,452,697 entries, and the total number of residues reached 1,052,890,111.

FTP site for DB download
DDBJ Rel. 67 Completed Sep. 29, 2006
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public. We completed DDBJ Release 67 in Sep. 30, 2006. DDBJ Release 67 consists of 61,144,621 entries, and the number of bases reached 65,443,024,193.

FTP site for periodical release and new data download

Report for The 19th International Collaborators Meeting Sep. 29, 2006
DDBJ, EMBL-Bank/EBI, GenBank/NCBI hold the international collaborators meetings in every May for the porpose of the operation and the implement of the collaborative construction of the international nucleotide sequence database.

In the meeting, the three banks report each bank activities in the past year, and discussed some practical matters to maintain and to develop the nucleotide sequence database
under INSDC; International Nucleotide Sequence Database collaboration.

The report for The 19th International Collaborators Meeting was placed on the DDBJ HP. This report will also be provided in the DDBJ Mail Magazine No.28.
Genome Network Platform Data Update Sep. 28, 2006
Genome Network platform Data has been updated on September 29, 2006.

Reference URL:
http://genomenetwork.nig.ac.jp/index_e.html
Failure in part of search services in the WWW getentry Sep. 28, 2006
getentry is the entry retrieval system by accession numbers etc, which is provided by DDBJ via WWW and E-mail servers.

Recently, we found there were some entries, which had not been displayed on the web version of getentry for a certain period (see below for details).

The problem entries are contig entries released by DDBJ and GenBank. They include a part of the CON 7269 entries, corresponding to the release of 223 thousands WGS entries of the Medaka strain Hd-rR, released by DDBJ on April 20, 2006.

We kindly request users to conduct their searches again if you have used the web version of getentry in the affected period, using the relevant keywords. Currently, the web version of getentry works normally.

Fortunately, the e-mail version of getentry was not affected by this trouble.

Details are as follows:

  • Affected periods:
    [entries released by DDBJ] April 24, 2006 - May 24, 2006
    [entries released by GenBank] January 4, 2005* - May 24, 2006

    * Actual date is calculated by the first released date of noticed CH entries (e.g.CM00126)

  • Cause: bug at the web version searching program
  • Condition: Users could not get complete results during the affected period and in the following conditions.
    - when you specify:
    ID as [Accession],
    DATABASE as [Flat File (DDBJ)],
    Result as [WWW] and
    do the search with the relevant undisplayable entries in the query box.

  • Undisplayable entries:(-->see the accession numbers list)
    [entries released by DDBJ] 1121 entries
    [entries released by GenBank] 1092 entries
We deeply apologize for any inconveniences that this may have caused to our users.
We will try to set the preventive measures to cope with these troubles immediately.

Genome data was added to GIB Sep. 28, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the genome sequence data of Francisella tularensis subsp. holarctica OSU18 (by Baylor College of Medicine) was released, we incorporated them to GIB, and now you can search those data.
Genome data was added to GIB Sep. 21, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the genome sequence data of Hyphomonas neptunium ATCC 15444 (by The Institute for Genomic Research) was released, we incorporated them to GIB, and now you can search those data.

Release of new Porcine full length cDNA 10,000 entries Sep.20, 2006
DDBJ newly released Porcine cDNA 10,000 entries, which had been submitted by National Institute of Agrobiological Sciences. These entries were released as DDBJ daily updates on Sep.16, 2006.

Reference URL: http://pede.dna.affrc.go.jp/

The accession numbers and the file names for anonymous FTP are as follows;

  • AK230469-AK240615 (10147 entries)
  • anonymous FTP:
    Sus_scrofa_HTC_060916_1.seq.gz
Genome data was added to GIB Sep. 19, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the genome sequence data of Granulobacter bethesdensis CGDNIH1 (by NIH), Nitrosomonas eutropha C71, Shewanella frigidimarina NCIMB 400, Syntrophomonas wolfei subsp. wolfei str. Goettingen and Maricaulis maris MCS10 (by JGI) were released, we incorporated them to GIB, and now you can search those data.
Genome data was added to GIB Sep. 15, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the genome sequence data of Alkalilimnicola ehrlichei MLHE-1 (by IJoint Genome Institute) was released, we incorporated them to GIB, and now you can search those data.

Apology for the Defect of the result display in WWW getentry Sep. 14, 2006
getentry is the entry retrieval system by accession numbers etc,
which is provided by DDBJ via WWW
and E-mail servers.

Duinrg the following period, there were some search results in which a part of the
entry was not displayed in the screen.

  • Period: September 5, 2006 17:00 - September 6, 2006 16:00 (JST)
If you did the search using getentry during the above period, please do it again.

The defect had already been fixed, and now, the service works normally.
E-mail version getentry was not affected.

We apologize for your inconvenience.

NIG network service temporary down due to electric power interruption Sep. 11, 2006
NIG network service was affectd by the electric power
interruption which had occured on September 11 midnight.
Details are as follows:

Period: May 11 (Mon) 03:19 - 03:52 (JST)
Affectd service: NIG network service

Now the service works normally. We apologize for your inconvenience.

Update of "Conference on Information Biology" Sep. 5, 2006
Following conferences were added to "Conference on Information Biology"

2006

2007

  • Bioinformatics
    Research and Development (3/12-14)
  • 3rd IEEE Symposium on Computational Intelligence in
    Bioinformatics and
    Computational Biology (4/1-5)
  • ISBRA
    2007
    (5/6-9)
  • 23rd
    International Conference on Yeast Genetics and Molecular Biology
    (7/1-6)
  • ISMB/ECCB (7/19-25)
  • Computational Systems Bioinformatics (8/13-17)
Genome data was added to GIB Sep. 4, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the genome sequence data of Synechococcus sp. CC9311 (by The Institute of Genomic Research), Shewanella sp. MR-4 and Shewanella sp. MR-7 (by Joint Genome Institute) were released, we incorporated them to GIB, and now you can search those data.
Genome data was added to GIB Sep. 1, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the genome sequence data of Ralstonia eutropha H16 (by Goettingen Genomics Laboratory) was released, we incorporated them to GIB, and now you can search those data.

Redistribution of genomic sequence (build 3) of the cultivar Nipponbare of Oryza sativa ssp. japonica assigned with RAP annotation Sep. 1, 2006
The entries corresponding to complete sequences of japonica rice chromosomes were updated. Their accession numbers are AP008207-AP008218. The updated contents were the results annotated by The First Rice Annotation Project Meeting (RAP1) which was an international rice genome annotation project organized by Japanese research groups.

By this updating, AP008207-AP008218 entries were redistributed with approximately 26,800 CDS (protein coding region) features.

This data can be acquired from the following sites.

The result of RAP1 annotation has also been available in the Rice Annotation Project Database (RAP-DB) at the National Institute of Genetics.

(References)

Genome data was added to GIB Aug. 28, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the genome sequence data of Haemophilus somnus 129PT (by Joint Genome Institute) was released, we incorporated them to GIB, and now you can search those data.
PRF Rel. 110 was releasedAug. 14, 2006
PRF (Protein Research Foundation)/SEQ database Release 110 was released on Aug. 14, 2006 at DDBJ. PRF Release 110 consists of 632,307 entries, and the total number of residues reached 218,939,855.
Genome data was added to GIB Aug. 14, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the genome sequence data of Pseudomonas entomophila L48 (by Genoscope) was released, we incorporated them to GIB, and now you can search those data.
Genome data was added to GIB Aug. 8, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the genome sequence data of Bordetella avium 197N (by Sanger Institute), Frankia alni ACN14a (by Genoscope) were released, we incorporated them to GIB, and now you can search those data.
Genome data was added to GIB Aug. 8, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the genome sequence data of Clostridium perfringens ATCC 13124 was released by The Institute for Genomic Research, we incorporated it to GIB, and now you can search those data.
Genome data was added to GIB Aug. 4, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the genome sequence data of Borrelia afzelii PKo was released by Fritz Lipmann Institute, we incorporated it to GIB, and now you can search those data.
Genome data were added to GIB Aug. 4, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the genome sequence data of Clostridium perfringens SM101 (by The Institute for Genomic Research), Rhodococcus sp. RHA1 (by University of British Columbia) were released, we incorporated them to GIB, and now you can search those data.

Release of 53,359 EST entries for honey bee Jul. 31, 2006
DDBJ newly released 53,359 EST entries for honey bee (Apis mellifera), which had been submitted by RIKEN Genomic Sciences Center. These entries were released as DDBJ daily update on 7/28..

Reference URL: http://genome.gsc.riken.jp/

The accession numbers and the file names for anonymous FTP are as follows;

  • DB728206-DB781564 (53,359 entries)
  • anonymous FTP:
    Apis_mellifera_EST_060728_1.seq.gz
Genome data was added to GIB Jul. 31, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the genome sequence data of Clostridium perfringens ATCC 13124 was released by The Institute for Genomic Research, we incorporated it to GIB, and now you can search those data.
Statistics [Top 30 organisms according to the total number of nucleotides]
Update Jul. 27, 2006
Top 30 organisms according to the total number of nucleotides (-DDBJ rel.66)
in Breakdown
statistics was updated with releasing DDBJ rel.66.
Click the organismname to view the graph of change.
Update of databases related to the H-Invitational Jul. 25, 2006
The mirror H-Invitational Database (H-InvDB) was upgraded on July 7, 2006. The latest version 3.4 of H-InvDB is now available.
Genome data was added to GIB Jul. 25, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.

Because the genome sequence data of Alcanivorax borkumensis SK2 was released by German Research Center for Biotechnology, we
incorporated it to GIB, and now you can search those data.
Genome data was added to GIB Jul. 25, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.

Because the genome sequence data of Shigella flexneri 5 8401 was released by Chinese Ministry of Public Health, we
incorporated it to GIB, and now you can search those data.
DAD rel. 36 was released Jul 19, 2006
DDBJ amino acid database (DAD) Release36 was released on Jul. 19, 2006 at DDBJ. DAD Release 36 consists of 3,223,773 entries, and the total number of residues reached 986,599,459.

FTP site for DB download
Genome data was added to GIB Jul. 19, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the genome sequence data of Escherichia coli 536 was released by Goettingen Genomics Laboratory, we incorporated it to GIB, and now you can search those data.
Genome data were added to GIB Jul. 19, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the genome sequence data of Francisella tularensis subsp. tularensis FSC 198 (by University of Birmingham), Cytophaga hutchinsonii ATCC 33406 and Mesorhizobium sp. BNC1 (by Joint Genome Institute) were released, we incorporated them to GIB, and now you can search those data.
Minerva periodic maintenance Jul. 14, 2006
Minerva service will be unavailable during the following date because of the periodic maintenance. Thank you very much for your understanding and cooperation.

July 21, 2006 (Fri) 12:00- 21:00
Version-up of BLAST 2006.7.12
BLAST and PSI-BLAST of DDBJ homology search services provided through web and e-mail were updated today.

  • BLAST, PSI-BLAST Version number: 2.2.13-> 2.2.14

ClustalW web screen lay-out change and new additional function July 12, 2006
DDBJ provides ClustalW services through WWW and E-mail. In the WWW ClustalW , we modified the data submit screen lay-out, and added some new options as follows.

  • "Sequence input box" is transferred to the top of the page.
  • "TYPE" options became independent from "ALIGN" options group.
  • "AUTOMATIC" was newly added to the the "TYPE" options.
    * When the "AUTOMATIC" is specified in the "TYPE" option, the ClustalW program identifies the sequence type (DNA/Protein) automatically and does the analysis using all default values.

  • "p-distance"was added to the parameters of "DISTANCE" option.
  • "KIMURA" option was integrated into the "DISTANCE" option.
Illegal values were included in CONTIG lines of part of ultra-contig and chromosome entries derived from Oryzias latipes (Japanese medaka) WGS dataOctober 20, 2006
Part of ultra-contig and chromosome entries, which were constructed by using Oryzias latipes (Japanese medaka) WGS data, contained illegal values at the location of piece entries in CONTIG lines.

  • The accession and version numbers of wrong ultra-contig and chromosome entries were listed below. At present, all the wrong entries were replaced with corrected ones. The version number of the corrected ultra-contig entries is ".4".

    List of accession and version numbers of the wrong ultra-contigs (42 entries)

    DF076134.3, DF076146.3, DF076156.3, DF076165.3, DF076168.3, DF076174.3,
    DF076189.3, DF076197.3, DF076201.3, DF076203.3, DF076205.3, DF076217.3,
    DF076230.3, DF076245.3, DF076247.3, DF076249.3, DF076256.3, DF076258.3,
    DF076269.3, DF076279.3, DF076281.3, DF076285.3, DF076298.3,
    DF076306.3,
    DF076312.3, DF076313.3, DF076318.3, DF076341.3, DF076366.3, DF076379.3,
    DF076386.3, DF076387.3, DF076391.3, DF076408.3, DF076411.3,
    DF076417.3,
    DF076418.3, DF076425.3, DF076430.3, DF076449.3, DF076456.3, DF076457.3

    List of accession and version numbers of the wrong chromosome (20 entries)

    DG000001.1, DG000002.1, DG000003.1, DG000004.1, DG000005.1,
    DG000006.1,
    DG000008.1, DG000009.1, DG000010.1, DG000011.1, DG000012.1, DG000013.1,
    DG000014.1, DG000016.1, DG000018.1, DG000019.1, DG000021.1, DG000022.1,
    DG000023.1, DG000024.1

We have replaced 24 entries of all chromosomes with updated version like below in order to control the chromosome versions uniformly.

previous version   updated version
DG000001.1-DG000024.1 --> DG000001.3-DG000024.3
DG000001.2-DG000024.2 --> DG000001.4-DG000024.4
DG000001.2-DG000024.2 were transferred to DG000001.4-DG000024.4 without any changes except for the date of LOCUS line and version number
The below three files, which were distributed from our anonymous FTP site:
ftp://ftp.ddbj.nig.ac.jp/ddbj_database/mass/Oryzias_latipes_CON/, contain the entries including the illegal CONTIG lines. Please be careful not to use the three files. At present, the three files were removed from the FTP site and replaced with the revised files.

ftp://ftp.ddbj.nig.ac.jp/ddbj_database/mass/Oryzias_latipes_CON/
Oryzias_latipes_CON_060524_1.seq.gz
Oryzias_latipes_CON_060531_1.seq.gz
Oryzias_latipes_CON_060605_1.seq.gz

  • You can see the revised file list by clicking here.

  • In addition, Oryzias_latipes_CON_060615_1.seq.gz that includes DG000001.2-DG000024.2 was replaced with Oryzias_latipes_CON_061018_1.seq.gz that includes DG000001.4-DG000024.4.
We apologize for your inconvenience.
Termination of providing the Blast program on NIG supernig server July 12, 2006
DDBJ will terminate providing the Blast program service which has been provided through NIG supernig server as under test operation, as of July 31, 2006.

However, we remain providing BLASTDB which will be placed on $BLASTDB.

So, if you install the program by yourself, you can run it using this DB.

Blast program is available from the following URL:

http://ncbi.nih.gov/BLAST/download.shtml
Genome data was added to GIB Jul. 12, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the genome sequence data of Trichodesmium erythraeum IMS101 was released by Joint Genome Institute, we incorporated it to GIB, and now you can search those data.

Removal of "C.elegans chromosome data" from homology search database options July. 4, 2006
DDBJ provides homology searh services (FASTA, BLAST, SSEARCH) through WWW and E-mail. As of the end of June, "C.elegans chromosome data" was removed from DNA database options.
Update of "Conference on Information Biology" July. 4, 2006
Following conferences were added to "Conference on Information Biology"

2006

2007

Genome data was added to GIBJul. 4, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the genome sequence data of Pseudoalteromonas atlantica T6c was released by Joint Genome Institute, we incorporated it to GIB, and now you can search those data.

Change of searchable divisions in SRS Jul. 4, 2006
SRS (Sequence Retrieval System) is the keyword retrieval service provided by DDBJ WWW server. After the incorporation of DDBJ release 66 data into SRS database, EST and GSS divisions data will be removed from SRS DDBJRELEASE and DDBJNEW database.

Because of the time lag between DDBJ release date (66 was released on June 29) and its loading time to SRS database, this change will be practically refleted to the service around mid to the end of July.

Thank you for your understanding and cooperation.
Genome data was added to GIB Jul. 3, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the genome sequence data of Helicobacter acinonychis Sheeba was released by Penn State University, we incorporated it to GIB, and now you can search those data.
Genome data was added to GIB Jul. 3, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the genome sequence data of Clostridium difficile 630 was released by Sanger Institute, we incorporated it to GIB, and now you can search those data.
DDBJ Rel. 66 Completed Jun. 29, 2006
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public. We completed DDBJ Release 66 in June 29, 2006. DDBJ Release 66 consists of 58,176,628 entries, and the number of bases reached 62,945,843,881.

FTP site for periodical release and new data download
Genome data were added to GIB Jun. 26, 2006
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the genome sequence data of Haloquadratum walsbyi DSM 16790 (by Max-Planck-Institute), Roseobacter denitrificans OCh 114 (by JTranslational Genomics Research Institute) were released, we incorporated them to GIB, and now you can search those data.
PRF Rel. 109 was released Jun. 19, 2006
PRF (Protein Research Foundation)/SEQ database Release 109 was released on
Jun. 19, 2006 at DDBJ. PRF Release 109 consists of 577,805 entries,
and the total number of residues reached 202,941,848.

Release of 6970 CON entries for Medaka strain Hd-rR Jun. 19, 2006
DDBJ newly released 6970 Medaka strain Hd-rR CON entries, which had been
submitted by University of Tokyo.
They correspond to the Medaka WGS dataset released on 6/7.

Reference URL:
http://medaka.utgenome.org/

The accession numbers and the file names for anonymous FTP are as follows;

  • scaffold/CON DF076466-DF08320 (6741 entries)
        Oryzias_latipes_CON_060608_1.seq.gz

  • ultra/CON DF083207-DF08341 (205 entries)
       Oryzias_latipes_CON_060613_1.seq.gz

  • chromosome/CON DG000001-DG000024 (24 entries)
        Oryzias_latipes_CON_060615_1.seq.gz
These entries were released as DDBJ daily updates on 6/8, 6/13, 6/15,
respectively.

anonymousFTP

Correction for the "Release of new 31 thousand scaffold/CON entries for
Medaka strain Hd-rR (Apr.21)" Jun. 17, 2006
The anonymous FTP files corresponding to the announcement of April 21
("DDBJ newly released 7296 Medaka
strain Hd-rR CON entries")
has been replaced on June 8 because of
mess-ups of their gap lengths. The corrected announcement is as follows:

 

Release of new 31 thousand scaffold/CON entries for
Medaka strain Hd-rR
Apr. 21, 2006
DDBJ newly released 31 thousand Medaka strain Hd-rR scaffold/CON
entries, which had been submitted by University of Tokyo.
They correspond to the Medaka WGS dataset released on 4/11.

Reference URL:
http://medaka.utgenome.org/

The accession numbers are as follows;

DF038236-DF069193 (30958 entries)

These entries were released as DDBJ daily updates on 4/14.
All of the data can be retrieved at
anonymous FTP site (Oryzias_latipes_CON_060524_1.seq.gz).
 

We apologize for your inconvenience.
Genome data were added to GIB Jun. 13, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.

Because the genome sequence data of Myxococcus xanthus DK 1622
(by The Institute for Genomic Research), Rubrobacter xylanophilus DSM
9941
, Mycobacterium sp. MCS, Yersinia pestis Nepal516
and Yersinia pestis Antiqua (by Joint Genome Institute) were
released, we incorporated them to GIB, and now you can search those data.
Genome data was added to GIB Jun. 9, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.

Because the genome sequence data of Helicobacter pylori HPAG1
was released by Washington University School of Medicine, we
incorporated it to GIB, and now you can search those data.
Update of "Conference on Information Biology" Jun. 9, 2006
Following conferences were added to "Conference on Information Biology"

2006

2007

Release of new 223 thousand Medaka strain Hd-rR WGS entries Jun. 8, 2006
DDBJ newly released 223 thousand Medaka strain Hd-rR WGS entries, which
had been submitted by University of Tokyo.

Reference URL:
http://medaka.utgenome.org/

The accession numbers are as follows;

BAAF03000001-BAAF03223203 (223203 entries)

These entries were released as DDBJ daily updates on 6/7.

All of the data can be retrieved at
anonymous FTP site (Oryzias_latipes_WGS_060607_1.seq.gz)

Release of 7296 CON entries for Medaka strain Hd-rR Jun. 8, 2006
DDBJ newly released 7296 Medaka strain Hd-rR CON entries, which had been
submitted by University of Tokyo.
They correspond to the Medaka WGS dataset released on 4/21.

Reference URL:
http://medaka.utgenome.org/

The accession numbers and the file names for anonymous FTP are as follows;

  • scaffold/CON DF069194-DF076129 (6936 entries)
        Oryzias_latipes_CON_060525_1.seq.gz

  • ultra/CON DF076130-DF076465 (336 entries)
       Oryzias_latipes_CON_060531_1.seq.gz

  • chromosome/CON DG000001-DG000024 (24 entries)
        Oryzias_latipes_CON_060605_1.seq.gz
These entries were released as DDBJ daily updates on 5/25, 5/31, 6/5,
respectively.

* Please note some of these CON entries has been updated because of
mess-ups of their gap lengths.

anonymousFTP
Genome data was added to GIB Jun. 7, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.

Because the genome sequence data of Burkholderia cenocepacia AU 1054
was released by Joint Genome Institute, we incorporated it to GIB,
and now you can search those data.
Genome data was added to GIB Jun. 6, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.

Because the genome sequence data of Lactobacillus delbrueckii subsp
bulgaricus
was released by Genoscope, we incorporated it to GIB,
and now you can search those data.
Update of "Conference on Information Biology" May 25, 2006
Following conferences were added to "Conference on Information Biology"

Genome data was added to GIB May 25, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.

Because the genome sequence data of Silicibacter sp. TM1040
was released by Joint Genome Institute, we incorporated it to GIB, and
now you can search those data.
Genome data was added to GIB May 24, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.

Because the genome sequence data of Sphingopyxis alaskensis RB2256
was released by Joint Genome Institute, we incorporated it to GIB, and
now you can search those data.
NIG network service temporary down due to electric power interruption May 22, 2006
NIG network service affectd by the electric power
interruption which had occured on May 22.
Details are as follows:

  • Period: May 22 (Mon) 00:19 - 19:00 (JST)
  • Affectd service: NIG network service
Now the service works normally. We apologize for your inconvenience.
DDBJ services emergency suspension caused by network system failure May 22, 2006
Because of the network system failures, some DDBJ services are being
suspended now. Details are as follows.

  • Date and time: 16:00 on May 20- (JST)
  • Suspended services:
    ARSA, BLAST, ClustalW, FASTA, getentry, Lib score, LIBRA-I,
    PDB Retriever, PSI-BLAST, SQmatch, SRS, SSEARCH, SSthread

  • Date and time: 0:10 on May 22- (JST)
  • Suspended services:
    DDBJ HP, GIB, Mirroring H-InvDB, SAKURA, Txsearch,
    Vector Screening System
Resume of the services will be announced on the DDBJ HP.
Thank you very much for your understanding and cooperation.

 

The service was resumed
at 19:00 on May 23. We apologize for your inconvenience.
The genome data are available from GIB by FTP May 17, 2006
GIB (Genome Information Broker)
is the comprehensive data repository of complete genomes of the
microorganisms and eukaryota. The FTP download site was opened to the
public. The genome sequence and annotation are download-able strain
by strain from the top page of
GIB (http://gib.genes.nig.ac.jp/)
and also ftp://ftpgib.genes.nig.ac.jp/.
DDBJ services temporary down due to electric power interruption May 17, 2006
There are some services affectd by the electric power interruption
which had occured on May 12. Details are as follows:

  • Date and time: 21:42 on May 12
  • Affectd seervice: GIB
  • Extent of affection: GIB serviers were shutoff at the time of
    power interruption, and as the result, 185 organisms genome data have
    been unuvailable untile 9:00 on May 15. Now the service works normally.
We apologize for your inconvenience.
DDBJ services emergency suspension for maintenance May 15, 2006
The following services will be unavailable today because of the
maintenance.

Period: May 15 (Mon) 17:00- 18:00 JST

Suspended services: (*unavailable either via WWW, E-mail)

  • Anonymous FTP
  • Database retrieval (getentry, SRS, ARSA)
  • Search and Analysis (FASTA, BLAST, SSEARCH, ClustalW)
Thank you very much for your understanding and cooperation.

 

The service was
resumed (May 15 18:00).
ARSA maintenance May 12, 2006
ARSA
service will be unavailable during the following date because of the
maintenance. Thank you very much for your understanding and cooperation.

Period: May 18 (Thu) 9:00- 18:00 JST
Supernig periodic maintenance May 12, 2006
Supernig service will be unavailable during the following date because
of the periodic maintenance.
Thank you very much for your understanding and cooperation.

Period: May 19 (Fri) 9:00- 22:00 JST
Update of "Conference on Information Biology" May 12, 2006
Following conferences were added to "Conference on Information Biology"

2006

2007

Genome data were added to GIB May 11, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.

Because the following genome sequence data were released,
we incorporated them to GIB, and now you can search those data.

  • Rhizobium leguminosarum bv. viciae 3841 (by Sanger Institute)
  • Streptococcus pyogenes MGAS9429 (by NIH)
  • Streptococcus pyogenes MGAS10270 (by NIH)
  • Streptococcus pyogenes MGAS2096 (by NIH)
  • Streptococcus pyogenes MGAS10750 (by NIH)
  • Acidobacteria bacterium Ellin345 (by JGI)
  • Deinococcus geothermalis DSM 11300 (by JGI)
  • Lawsonia intracellularis PHE/MN1-00 (by University of Minnesota)
ARSA service emergency suspension May 10, 2006
ARSA (All-round Retrieval Sequence and Annotation) is the DDBJ's new
retreival system, which is characteristic in the point of "high-speed"
and "XML based search system.

Because of the hardware system failures, ARSA is being suspended now.
Details are as follows.

  • Current condition: Query submission is impossible, in spite of
    viewing the ARSA page.

  • Substitute service: You can use
    getentry
    (search by accession numbers) and
    SRS
    (search by keywords) as the substitutive services.

  • Resume: It will be announced on the DDBJ HP as soon as after the
    system is recovered.
Thank you very much for your understanding and cooperation.

 

The service was resumed
at 17:00 on May 10. We apologize for your inconvenience.
Genome data was added to GIB May 9, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.

Because the genome sequence data of Baumannia cicadellinicola Hc
(Homalodisca coagulata)
was released by The Institute for Genomic
Research, we incorporated it to GIB, and now you can search those data.
DDBJ services emergency suspension caused by network system failure May 8, 2006
Because of the network system failures, some DDBJ services are being
suspended now. Details are as follows.

Suspended services (*unavailable either via WWW, E-mail)

  • Anonymous FTP
  • Database retrieval (getentry, SRS, ARSA)
  • Search and Analysis (FASTA, BLAST, SSEARCH, ClustalW)

Resume of the services will be announced on the DDBJ HP.
Thank you very much for your understanding and cooperation.

 

The services were
resumed at 20:00 on May 8.
We apologize very much for your long-time inconvenience.
Release of additional human CAGE data (MGA entry) May 2nd, 2006
DDBJ newly distributed 1.89 million entries of human originated
short-transcript sequences as MGA (Mass sequence for Genome Annotation).

Those data have been submitted by RIKEN Genome Sciences Center.

All of MGA entries can be downloaded and brief explanation of a published
MGA data is displayed on the following URL, respectively.

Anonymous FTP

The related URL for this issue

Notice for SAKURA system suspension May 2nd, 2006
SAKURA
is a nucleotide sequence data submission system through the WWW server at DDBJ.

In order to conduct the server maintenance, SAKURA system will be
stopped the following date:

ftom May 9(Tue) 9:00 to May 10(Wed) 9:00 (JST)

We would appreciate your understanding and cooperation in advance.
Genome data was added to GIB May 2nd, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.

Because the genome sequence data of Ralstonia metallidurans CH34
was released by Joint Genome Institute, we incorporated it to GIB, and
now you can search those data.
Suspension of some parts of DDBJ activities during Japanese holidays Apr. 28, 2006
We at DDBJ suspend our business for releasing data and answering all
inquires from May 3 to 7, 2006.

Search and analysis services are available.

We will resume the normal business from May 8.
Thank you very much for your understanding and cooperation.
Update of databases related to the H-Invitational Apr. 28, 2006
The mirror H-Invitational Database (H-InvDB) was updated and released today. The version of mirror H-Invitational
Database (H-InvDB) rise "3.0".
Release of Genome Network Platform official portal site Apr. 27, 2006
Genome Network Platform official web site was released on January 25,
2006. The Genome Network Platform is one of the strategic research
programs of Genome Network Project.
This site have been updated on April 21, 2006.

Reference URL: http://genomenetwork.nig.ac.jp/index_e.html
Genome data was added to GIB Apr. 26, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.

Because the genome sequence data of Psychrobacter cryohalolentis K5
was released by Joint Genome Institute, we incorporated it to GIB,
and now you can search those data.

Release of new 223 thousand Medaka strain Hd-rR WGS entries Apr. 21, 2006
DDBJ newly released 232 thousand Medaka strain Hd-rR WGS entries,
which had been submitted by University of Tokyo.

Reference URL: http://medaka.utgenome.org/

The accession numbers are as follows;

BAAF02000001-BAAF02223025 (223025 entries)

These entries were released as DDBJ daily updates on 4/19.
All of the data can be retrieved at
anonymous FTP site
(Oryzias_latipes_WGS_060419_1.seq.gz).

Release of new 31 thousand scaffold/CON entries for Medaka strain Hd-rR Apr. 21, 2006
DDBJ newly released 31 thousand Medaka strain Hd-rR scaffold/CON entries,
which had been submitted by University of Tokyo.
They correspond to the Medaka WGS dataset released on 4/11.

Reference URL: http://
medaka.utgenome.org/

The accession numbers are as follows;

DF038236-DF069193 (30958 entries)

These entries were released as DDBJ daily updates on 4/14.
All of the data can be retrieved at anonymous FTP site (Oryzias_latipes_CON_060414_1.seq.gz).*

*Please note the file has been replaced on 6/8 because of mess-ups of their gap lengths(The corrected file name:Oryzias_latipes_CON_060524_1.seq.gz).
getentry result output failure in anonymous FTP Apr. 21, 2006
getentry
is the entry retrieval system by accession numbers etc, which is provided
by DDBJ via WWW and E-mail servers.

Because of the system error, the search results were not outputed when
"FTP" option was selected for obtaining results during the following period.

Other two options "WWW" and "E-mail" were not affected by this problem.

Period: April 18, 2006 14:00 - April 20, 2006 18:00 (JST)

Now, the service works normally. We apologize for your inconvenience.
Genome data were added to GIB Apr. 20, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.

Because the genome sequence data of Nitrobacter hamburgensis X14 and
Chromohalobacter salexigens DSM 3043 were released by Joint Genome
Institute, we incorporated them to GIB, and now you can search those data.
NIG Network services temporary down Apr. 19, 2006
NIG (National Institute of Genetics) network service will be unavailable
at the following schedule because of the network maintenance.

DDBJ network services and NIG supercomputer (supernig and minerva)
service will also be unavailable.

Thank you very much for your understanding and cooperation.

From April 26 (Web) 16:00 to 18:00 (JST)
Statistics [Top 30 organisms according to the total number of nucleotides] Update Apr. 14, 2006
Top
30 organisms according to the total number of nucleotides (-DDBJ rel.65)
in Breakdown
statistics was updated with releasing DDBJ rel.65.
Aedas aegypti (Yellow fever mosquito) was newly ranked in Top 30.
Click the organismname to view the graph of change.
Genome data were added to GIB Apr. 13, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.

Because the following genome sequence data were released by JGI, we
incorporated them to GIB, and now you can search those data.

Burkholderia xenovorans LB400, Methanococcoides burtonii DSM
6242
, Methylobacillus flagellatus KT, Polaromonas sp.
JS666
, Shewanella denitrificans OS217, Rhodopseudomonas
palustris BisB5

Release of new 232 thousand Medaka strain Hd-rR WGS entries Apr. 12, 2006
DDBJ newly released 232 thousand Medaka strain Hd-rR WGS entries,
which had been submitted by University of Tokyo.

Reference URL: http://medaka.utgenome.org/

The accession numbers are as follows;

BAAF01000001-BAAF01232667 (232667 entries)

These entries were released as DDBJ daily updates on 4/11.
All of the data can be retrieved at anonymous FTP site (Oryzias_latipes_WGS_060411_1.seq.gz).
PRF Rel. 108 was released Apr. 12, 2006
PRF (Protein Research Foundation)/SEQ database Release 108 was released on
Apr. 11, 2006 at DDBJ. PRF Release 108 consists of 555,007 entries, and
the total number of residues reached 195,762,527.
Genome data were added to GIB Apr. 10, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.

Because the genome sequence data of Escherichia coli UTI89 (by
Washington University School of Medicine) and Rickettsia bellii
RML369-C
(by CNRS) were released, we incorporated them to GIB,
and now you can search those data.
Notice for the termination of S&W SEARCH sercice by DDBJ Apr. 10, 2006
S&W SEARCH, one of the homology search services provided through web and
e-mail server by DDBJ was terminated on April 7, 2006.

As was already notified in the preliminary notice issued on February 18,
2005, because of dissolution of the manufacturing company which had
provided the hardware for the S&W SEARCH service, the disrupt which have
been going on since March 22 is no longer recovered.

As the substitute service,
SSEARCH
which runs by similar algorithm with S&W SEARCH are also provided by DDBJ,
and this service is continuously available.

DDBJ appreciate very much for your access to S&W SEARCh service over
the past long years.
Update of databases related to the H-Invitational Apr. 7, 2006
The content of databases related to the H-Invitational was updated.
The main content of the update is the following.

  1. The number of cDNA entry has increased 167,992 from 56,419

  2. The number of LOCUS entry has increased 35,005 from 25,585
  3. Version of mirror H-Invitational Database (H-InvDB)* become "3.0".
*Mirror H-InvDB will be updated in a few days.

Databases related to the H-Invitational

Release of new 243 thousand wheat EST entries Apr. 6, 2006
DDBJ newly released 243 thousand wheat EST entries, which had been
submitted by Kyoto Prefectural University.
The accession numbers are as follows;

CJ493525-CJ736986 (243462 entries)

All of the data can be retrieved at
anonymous FTP site.

Triticum_aestivum_EST_20060404_1.seq.gz
ARSA service temporary down Apr. 5, 2006
ARSA (All-round Retrieval of Sequence and Annotation) is the keyword search system provided by DDBJ under trial operation.

Because of the system maintenance, ARSA service will be unavailable
at the following schedule. During this period,
SRS and
getentry
will be helpful to you instead of ARSA.

Unavailable period: Apr. 12 (Wed), 2006 9:00 - 22:00 (JST)

Thank you very much for your understanding and cooperation on such
short notice.
Update of "Conference on Information Biology" Apr. 3, 2006
Following conferences were added to "Conference on Information Biology"

Genome data was added to GIB Apr. 3, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.
Because the genome sequence data of Lactobacillus salivarius subsp.
salivarius UCC118
was released by University College Cork, we
incorporated it to GIB, and now you can search those data.
DDBJ Rel. 65 Completed Apr. 3, 2006
The nucleotide sequence database collected and maintained by DDBJ is
quarterly released online to the public.
We completed DDBJ Release 65 in March 30, 2006.
DDBJ Release 65 consists of 55,890,995 entries, and the number of bases
reached 60,564,721,635.

FTP site for
periodical release and new data download
Termination of DDBJ/CIB Human Genomics Studio by DDBJ Mar. 31st, 2006
As was preliminarily anounced, DDBJ/CIB Human Genomics Studio service
provided through web server by DDBJ was terminated on March 31, 2006,
because of the hardware disorder.

H-Invitational Database
CIB-DDBJ Flat File Server is can be substituted for DDBJ/CIB Human
Genomics Studio.
Thank you very much for your understanding and cooperation.
Genome data was added to GIB Mar. 27, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences. Because the genome sequence data of
Rhodopseudomonas palustris BisB18 was released by JGI, we
incorporated it to GIB, and now you can search those data.
S&W SEARCH" service temporary down Mar. 22, 2006
Because of the server trouble, S&W SEARCH service is unavailable now.
The recovery of the system will be notified on this page as soon as
the reparing works are finished.

We apologize for the inconvenience.
Genome data was added to GIB Mar. 22, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.
Because the genome sequence data of Saccharophagus degradans 2-40
was released by JGI, we incorporated it to GIB, and now you can search
those data.
Genome data were added to GIB Mar. 20, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.
Because the genome sequence data of Chlamydophila felis Fe/C-56
(by Kitasato University), Desulfitobacterium hafniense Y51
(by RITE) and Rhodoferax ferrireducens DSM 15236 (by JGI) were
released, we incorporated them to GIB, and now you can search those data.
Genome data was added to GIB Mar. 17, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.
Because the genome sequence data of Francisella tularensis subsp.
holarctica LVS
was released by Oak Ridge National Laboratory, we
incorporated it to GIB, and now you can search those data.
Keyword search results error on SRS "AUTHORS" and "TITLE" fields Mar. 16, 2006
SRS
is one of the keyword search service provided through web server by DDBJ.

The failures were found in index files.

If you used SRS during the following period specifying "DDBJRELEASE" as
the target database, a part of the"AUTHORS" and "TITLE" fields were
not searched.

Therefore your search result might not be correct.

Now, the service is available without any problem.
The details are as follows.

  • Affected database and search field
    In "Quick Search" : DDBJRELEASE were selected as the Sequence
    libraries
    In "Advanced Search" : DDBJRELEASE and/or DDBJ were selected
    as the Sequence libraries, and any one (or more) of "AllText",
    "Authors", and "Title" was/were specified as search field

  • Affected period:
    In "Authors" field: October 2004 - March 13, 2006
    In "Title" field: February 2006 - March 13, 2006

  • Measure: Index files revisions were completed on March 13, 2006
We apologize for the inconvenience.
Release of new 136 thousand Human EST entries Mar. 14, 2006
DDBJ newly released 136 thousand Human EST entries, which had been
submitted by RIKEN Genomic Sciences Center.
The accession numbers are as follows;

DB441779-DB577968 (136190 entries)

These entries were released as DDBJ daily updates on 3/14.

All of the data can be retrieved at
anonymous FTP site.

Homo_sapiens_EST_20060314_1.seq.gz
New functions are added to "getentry" web server Mar. 13, 2006
"getentry" is the entry retrieval system by accession numbers etc, which
is provided by DDBJ via WWW and E-mail servers.

In the getentry web server, to obtain the results, there are 3 ways
(interactively, by E-mail, by anonymous FTP) provided. Among them, when
"anonymous FTP" is selected, up to 100,000 entries can be downloaded as
anonymous FTP by clicking the file name shown in the screen. Although it
may take a lot of time to make the result file for anonymous FTP in case
of a big volume file, there has been a problem that the progress of the
file making could not been checked so far.

To solve this problem, since March 13, 2006, the following 2 functions
are newly equipped for the anonymous FTP.

  1. Check of the status of the file making
    please click "the state of making the file" in the lower frame part,
    then the message showing the file making status are displayed.

  2. Sending the E-mail notifying the completion of the file making for
    FTP

    If you enter your E-mail address, the E-mail to notify the completion
    of the file making will be sent to you.
Both are very useful when you use anonymous FTP to obtain the getentry
retrieval results.
Genome data was added to GIB Mar. 3rd, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.
Because the genome sequence data of Jannaschia sp. CCS1 was released
by JGI, we incorporated it to GIB, and now you can search those data.
Preliminary notice for the termination of DDBJ/CIB Human Genomics Studio by
DDBJ Mar. 2nd, 2006
DDBJ/CIB Human Genomics Studio service provided through web server by DDBJ
will be terminated on March 31, 2006, because of the hardware disorder.

H-Invitational Database
CIB-DDBJ Flat File Server is can be substituted for DDBJ/CIB Human
Genomics Studio.
Thank you very much for your understanding and cooperation.
System failure on Homology search services are recovered Feb. 27, 2006
The system failures in DDBJ's homology search services were recovered
on February 27 at 15:30. At present, the correct results are available.

Thank you very much for your understanding and cooperation.

  • Period : February 19, 2006 - February 27, 2006 15:30
  • Affected services :all homology search programs (WWW, E-mail) except
    for PSI-BLAST*
*Please note that S&W SEARCH takes a littel more time for the recovery
because the incorporation of the corrected database into S&W SEARCH
program requires more longer times than other services.

S&W SEARCH was resumed. At present, all
services work normally (02:15, Mar 1).
Update of "Conference on Information Biology" Feb. 27, 2006
Following conferences were added to "Conference on Information Biology"

  • International Workshop on the Interoperability of Biological Information Resources (IBIR) (3/17)
System failure on Homology search services Feb. 27, 2006
The system failures were found in DDBJ's
homology search
services.
If you used DDBJ's homology search services during the
following period, your search result might not be correct. The details
are as follows.

  • Period : February 19, 2006
    -

  • Affected services :all homology search programs (WWW, E-mail)
    except for PSI-BLAST

  • Affected database : nucleotide sequence database
  • Affected divisions : BCT (bacteria)
    GSS (genome survey sequences)
    INV¡Êinvertebrates¡Ë
    MAM¡Êmammals other than primates and rodents)
    PLN (plants)
    ROD¡Êrodents¡Ë
    SYN¡Êsynthetic DNAs¡Ë
    VRT¡Êvertebrates other than mammals¡Ë
    VRL¡Êviruses¡Ë
The recovery of the system will be notified on this page as soon as the
reparing works are finished. We apologize for the inconvenience.
Genome data were added to GIB Feb. 24, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.
Because the genome sequence data of Anaplasma phagocytophilum HZ,
Ehrlichia chaffeensis Arkansas and Neorickettsia sennetsu
Miyayama
(by TIGR) were released, we incorporated them to GIB,
and now you can search those data.
FTP server emergency maintenance Feb. 22, 2006
Because of the urgent maintenance of DDBJ's FTP server, following
services are unavailable now.
Thank you very much for your understanding and cooperation.

Feb. 22, 2006 (Wed) 15:00- 17:00

Unavailable services: getentry, SRS, Anonymous FTP, SQmatch
Genome data were added to GIB Feb. 20, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.
Because the genome sequence data of Staphylococcus aureus subsp. aureus
NCTC 8325
(by The University of Oklahoma Health Sciences Center) and
Methanospirillum hungatei JF-1 (by Joint Genome Institute) were
released, we incorporated them to GIB, and now you can search those data.
Genome data were added to GIB Feb. 15, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.
Because the genome sequence data of Novosphingobium aromaticivorans
DSM 12444
(by JGI) and Staphylococcus aureus subsp. aureus
USA300
(by University of California) were released, we incorporated
them to GIB, and now you can search those data.
Homology search error at X. tropicalis of EST division Feb. 13, 2006
In DDBJ's homology search programs (WWW, E-mail), divisions can be
specified as one of the search option, and furthermore, in the EST
division, organisms can be selected from 21 organisms which are listed
based on the submitted-numbers' statistics (this option is effective only
when "DDBJ ALL" or "DDBJ updates" is selected). Silurana tropicalis,
one of the 21 EST organisms was merged into Xenopus tropicalis in
2004.

But, we missed taking this change into database construction processes,
and also did not change the description of the search page.
Therefore, X. tropicalis have not been able to be selected as
the EST organism, and the search being selected S. tropicalis have not
been made properly.

Detaiils are as follows.

  • Period: 2004.07. - 2006. 01.20
  • Affected databases: all homology search programs (WWW, E-mail)
    except for PSI-BLAST.

  • Situation: When S. tropicalis of EST was specified as a
    division, the search did hit no results (when "select-all" or "others"
    of EST division was selected, the correct results were obtained.)

  • Correction: database construction program bug was fixed.
    Descriptions of the search pages and their help pages were revised.
    Now the correct search results are available. Furthermore, the check
    program to prevent reoccurrence of the trouble will be introduced.
We apologize for the service error over the long period.
Minerva periodic maintenance Feb. 13, 2006
Minerva service will be unavailable during the following date because
of the periodic maintenance.
Thank you very much for your understanding and cooperation.

Feb. 17, 2006 (Fri) 12:00- 21:00
Statistics [Top 30 organisms according to the total number of nucleotides] UpdateFeb. 10, 2006
Top 30 organisms
according to the total number of nucleotides (-DDBJ rel.64)
in Breakdown
statistics was updated with releasing DDBJ rel.64. Ovis aries
(sheep) and Gasterosteus purpuratus (threespined stickleback)
was newly ranked in Top 30.
Click the organismname to view the graph of change.
Update of "Conference on Information Biology" Feb. 10, 2006
Following conferences were added to "Conference on Information Biology"

  • MGED9-The
    Meeting of the Microarray Gene Expression Data Society (9/7-10)
Genome data were added to GIB Feb. 9, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.
Because the genome sequence data of Cyanobacteria bacterium Yellowstone
A-Prime
, Cyanobacteria bacterium Yellowstone B-Prime
(by TIGR), and Frankia sp. CcI3, Rhodopseudomonas palustris
HaA2
(by JGI) were released, we incorporated them to GIB, and now
you can search those data.
H-Invitational Databases were updated Feb 8, 2006
At Jan. 27th, 2006, the contents of
H-Invitational Database
CIB-DDBJ Flat File Server and
Mirroring H-Invitational
Database (H-InvDB)
(Release number: H-InvDB_2.4) were updated.

The new features include:

- updates of IDs of the external databases (HUGO/Entrez Gene).

- alternative splicing isoforms (pattern classification).
Genome data were added to GIB Feb. 7, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.
Because the genome sequence data of Anaeromyxobacter dehalogenans
2CP-C
(by Joint Genome Institute) and Syntrophus aciditrophicus
SB
(by Integrated Genomics Inc.) were released, we incorporated them
to GIB, and now you can search those data.
Update of "Conference on Information Biology" Feb.3 , 2006
Following conferences were added to "Conference on Information Biology"

ClustalW web server temporary down Feb. 3, 2006
ClustalW
is a multiple alignment and tree-making program provided through web
and e-mail servers by DDBJ.

ClustalW web service was unavailable during the following date because
of the disk error.
Now, the service is available without any porblem.
We apologize for the inconvenience.

From Jan. 28 11:00 to Jan.29 0:00 (JST)
Genome data was added to GIB Feb. 3, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.
Because the genome sequence data of Rhizobium etli CFN 42
was released by Universidad S/N, Col. Chamilpa, we incorporated it to
GIB, and now you can search those data.
Release of new 780 thousand Rice EST entries Feb. 2, 2006
DDBJ newly released 780 thousand Rice (Oryza sativa (japonica
cultivar-group)) EST entries, which had been submitted by National
Institute of Agrobiological Sciences.

The accession numbers are as follows;

  • CI000001-CI778739
These entries were released as DDBJ daily updates from Jan. 31 to Feb. 2.

All of the data can be retrieved at anonymous FTP site.

- rice_EST1.seq.gz (CI000001-CI250000, 83MB)

- rice_EST2.seq.gz (CI250001-CI500000, 76MB)

- rice_EST3.seq.gz (CI500001-CI778739, 79MB)
Update of 1.6 million Human EST entries Feb. 2, 2006
DDBJ updated 1.6 million Human EST entries on their reference information
by the request for "The Institute of Medical Science The University of
Tokyo" and "Reverse Proteomics Research Institute Co.,Ltd".

The accession numbers of these entries are as follows;

  • AU116789-AU117215
  • AU117217-AU144110
  • AU144112-AU160826
  • AU279383-AU280837
  • BP192706-BP383670
  • DA000001-DA999999
  • DB000001-DB384947
These entries were released as DDBJ daily updates from 1/17 to 1/26.

All of the data can be retrieved, displayed and acquired by using the
DDBJ retrieval tool,
getentry.
Genome data was added to GIB Jan. 27, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.
Because the genome sequence data of Erythrobacter litoralis HTCC2594
was released by J. Craig Venter Institute, we incorporated it to GIB,
and now you can search those data.
Release of the complete genome sequence of Escherichia coli K-12 strain W3110 Jan. 24, 2006
The complete genome sequence of Escherichia coli K-12 strain W3110
was released from DDBJ. Accession number is
AP009048.

As to E. coli K-12 genome, the annotation workshop,
Monica Riley of
Marine Biological Laboratory (MBL)
worked as a leader,
was held in 2003 and 2005 at MBL. From Japan, the researchers of
NAIST,
NIBB
and DDBJ participated in the workshop. An accurate and
completeness annotation were assigned to the most recent and
exact genome sequences of two E. coli K-12 strains
(strain W3110 and MG1655 whose genome sequences were
determined in Japan and U.S.A, respectively).

The result of the workshop has been already published as a paper in
Nucleic Acids Research.

Riley, M., et al. "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005", Nucleic Acids Res., 34, 1-9 (2006).

E. coli is one of the most important organisms for
various biological fields, such as molecular biology, genome
sequencing, systems biology, etc. The release of accurate and
completeness E. coli genome annotation provide
researchers with meaningful information in the science field.

Reference URL:

Functional Genomic Analysis of E. coli in Japan

MBL News

GIB Escherichia coli K-12 W3110
Genome data were added to GIB Jan. 19, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.
Because the genome sequence data of Sodalis glossinidius morsitans
(by Kitasato University) and Aster yellows witches'-broom phytoplasma
AYWB
(by The Ohio State University) were released, we incorporated
them to GIB, and now you can search those data.
ARSA service resumed Jan. 19, 2006
ARSA (All-round Retrieval of Sequence and Annotation) is the keyword search system provided by DDBJ under trial operation.

The service which had been unavailable because of the system upgrade
maintenance works was resumed. According to this upgrade works, the
following points are improved in the service.

- ARSA can be provided 24 hours without break

- Results (Flatfile, XML) are displayed faster than before

Thank you for your understanding against the inconvenience of the
interception.
Report for DDBJ activicies in NAR Jan. 18, 2006
The new and significant DDBj activities of the past year were introduced
in the following 3 papers appeared in Nucleic Acids Research Vol.34
Database Issue (Jan. 1).
  • Report for Overall activities of DDBJ in 2005
    "DDBJ in preparation for overview of research activities behind
    data submissions."

    Kousaku Okubo, Hideaki Sugawara, Takashi Gojobori and Yoshio Tateno
    Nucleic Acids Research, 2006, Vol. 34, Database issue D6-D9
    (Summary) INSDC collaboation¡¤introduction of newly released databases,
    New development, especially , indexing for breakdown statistics are
    released in DDBJ HP. (PMID: 16381940)

  • Introduction of the new database:BodyMap-Xs
    "BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for
    cross-species comparison of gene expression."

    Osamu Ogasawara, Makiko Otsuji, Kouji Watanabe, Takayasu Iizuka,
    Takuro Tamura, Teruyoshi Hishiki, Shoko Kawamoto, and Kousaku Okubo
    Nucleic Acids Research, 2006, Vol. 34, Database issue D628-D631
    (Summary) BodyMap-Xs (a database for cross-species gene expression
    comparison based on EST data) was created and released.(PMID: 16381946)

  • Introduction of the new database:Rap-DB
    "The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa
    ssp. japonica genome information."
    br>
    Hajime Ohyanagi, Tsuyoshi Tanaka, Hiroaki Sakai, Yasumasa Shigemoto,
    Kaori Yamaguchi, Takuya Habara, Yasuyuki Fujii, Baltazar A. Antonio,
    Yoshiaki Nagamura, Tadashi Imanishi, Kazuho Ikeo, Takeshi Itoh, Takashi
    Gojobori, and Takuji Sasaki
    Nucleic Acids Research, 2006, Vol. 34, Database issue D741-D744
    (Summary) The RAP-DB, a database for highly curated rice annotations was
    opened in last December..
    (PMID: 16381971)
Genome data was added to GIB Jan. 18, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota complete
genome sequences.
Because the genome sequence data of Xanthomonas oryzae pv. oryzae
MAFF 311018
was released by NIAS, we incorporated it to GIB, and
now you can search those data.
PRF Rel. 106 was released Jan. 18, 2006
PRF (Protein Research Foundation)/SEQ database Release 106 was released on
Jan. 17, 2006 at DDBJ. PRF Release 106 consists of 476,919 entries,
and the total number of residues reached 169,825,865.
Genome data was added to GIB Jan. 13, 2006
GIB (Genome Information Broker)
provides an integrated search of Bacteria, Archaea, Eukaryota completet
genome sequences. Because the genome sequence data of Methanosphaera
stadtmanae DSM 3091
was released by Goettingen Genomics Laboratory,
we incorporated it to GIB, and now you can search those data.
Supernig periodic maintenance Jan. 13, 2006
Supernig service will be unavailable during the following date because
of the periodic maintenance.
Thank you very much for your understanding and cooperation.

Jan. 20 (Fri) 10:00- 21:00 JST
DAD rel. 34 was released Jan. 12, 2006
DDBJ amino acid database (DAD) Release34 was released on Jan. 11, 2006
at DDBJ. DAD Release 34 consists of 2,799,119 entries,
and the total number of residues reached 859,887,417.

FTP site for DB download
Update of "Conference on Information Biology" Jan.12, 2006
Following conferences were added to "Conference on Information Biology"

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