What’s New(2009)

Apology for the failure of ClustalW running Dec 28, 2009
DDBJ provides ClustalW via WWW.

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

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

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

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

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

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

Closing H-Inv DB mirror site Dec. 8, 2009
CIB-DDBJ will close H-Invitational Database (H-Inv DB) mirror site as of Dec. 31, 2009.
Accordingly, anonymous-FTP will be shifted from the H-InvDB server to the DDBJ server.

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

Release of new Drosophila melanogaster small RNAs, MGA 48,002 entries Dec. 7, 2009
DDBJ newly released 48,002 entries of MGA data, Drosophila melanogaster small RNAs, which had been submitted by National Institute of Advanced Industrial Science and Technology.

The accession numbers  (Anonymous FTP)  are as follows ;

Reference sites

These entries were released as DDBJ daily updates on Dec. 4, 2009.

Exhibit the DDBJ booth in MBSJ 2009 Dec. 2, 2009
MBSJ 2009 (The 32nd Annual Meeting of the Molecular Biology Society of Japan) is being held at PACIFICO YOKOHAMA from Dec. 9(Wed) to 12(Sat). DDBJ has the booth in the exhibition that belongs to National Bio-resource Project (NBRP). The posters to introduce the activities and the services of DDBJ are displayed and some information paper is distributed there.

Release of new Vigna radiata WGS 46,645 entries Dec. 1, 2009
DDBJ newly released 46,645 entries of WGS data derived from Vigna radiata, which had been submitted
by National Center for Genetic Engineering and Biotechnology,Thailand.

The accession numbers  (Anonymous FTP)  are as follows ;

  • BABL01000001-BABL01046645 (BABL.gz) (46,645 entries)

Reference sites

These entries were released as DDBJ daily updates on Nov. 30, 2009.

DDBJ network services is unavailable for power outage Nov. 13, 2009
DDBJ network services including NIG supercomputer (supernig) will be unavailable at the following schedule because of the electric power outage. Please note that the suspended period depends on the service.

Services Scheduled (JST)
SAKURA Nov.27(Fri) 13:00 - Nov.30(Mon) 12:00(resumed)
getentry, ARSA,Homology Search System, ClustalW,

TXSearch, Vector Screening System,

Anonymous-FTP
Nov.27(Fri) 17:00 - Nov.30(Mon) 11:00 (resumed)
Mirroring H-Inv DB Nov.27(Fri) 17:00 - Nov.30(Mon) 11:00(resumed)
DDBJ HP Nov.27(Fri) 17:00 - Nov.29(Sun) 18:00 (resumed)
GIB Nov.27(Fri) 10:00 - Nov.30(Mon) 11:00(resumed)
NIG supercomputer (supernig) Nov.27(Fri) 17:00 - Nov.30(Mon) 9:00 (resumed)

Thank you for your cooperation and understanding.
All services were resumed. Thank you for your cooperation. (Nov. 30 at 11:00 JST)

Release of new tomato (Solanum lycopersicum) WGS 100,783 entries Nov. 9, 2009
DDBJ newly released 100,783 entries of WGS data derived from tomato (Solanum lycopersicum), which had been submitted
by Kazusa DNA Research Institute.

tomato

The accession numbers  (Anonymous FTP)  are as follows ;

  • BABP01000001-BABP01100783 (BABP.gz) (100,783 entries)

Reference sites

These entries were released as DDBJ daily updates on Nov. 6, 2009.

(Photo: Integrated Database Project)

Genome Information Broker (GIB) meets the Targeted Proteins Research Program (TPRP) Nov. 9, 2009
E. coli genomes in GIB are now equipped with an external link to eSOL (Solubility database of all E.coli proteins) that is a collaborative product of a protein production team and the information platform in TPRP.

gib

example

  • Escherichia coli str. K12 substr. W3110
  • Escherichia coli str. K12 substr. MG1655

ARSA database search partially unavailable Nov. 4, 2009
ARSA is a high-speed data retrieval system provided by DDBJ via WWW and Web API .Some DBs were not searchable during the following period. Details are as follows:

  • Date & Time: Nov. 3, 2009 (Tue) 11:30 - Nov. 4, 2009 (Wed) 13:30
  • Unavailable DBs: All DBs other than DDBJ and DAD (18 DBs)
  • Current condition: Currently, all DBs are searchable, but the data are as of October 25, 2009 (JST).
    The data recovery (update for the latest version) will be informed in this DDBJ HP.

Thank you for your understanding and cooperation.

Data recovery works finished. Thank you for your cooperation. (Nov. 5, 2009 at 13:30)

Apology for the bug of the Blast search result view Oct. 26, 2009
In the DDBJ's Blast service provided via WWW, a bug was fixed. The details are as follows:
  • Period: from Feb., 2009 to Oct. 22, 2009 (JST)
  • Service: BLAST
  • Condition: In the result view screen of "Text View" option, the horizontal line of the sequence and the corresponding check box (to select the sequence for the successive ClustalW analysis) was unmatched. As a result, in the following ClustalW analysis, when the "GO TO CLUSTALW" bottun was clicked, the sequence below the checked line was entered automatically. This defect was only in the result view screen, and the BLAST search result was all correct.
  • Measure: The bug had already been removed, and at present, the location of the sequence and the check box is viewed correctly.

DDBJ sincerely apologizes for your inconvenience during the long period.

Release of new eggplant (Solanum melongena) and turkey berry(Solanum torvum) EST 126,465 entries Oct. 20, 2009
DDBJ newly released 126,465 entries of EST data derived from eggplant (Solanum melongena) and turkey berry (Solanum torvum), which had been submitted by National Institute of Vegetable and Tea Science.

The accession numbers  (Anonymous FTP)  are as follows;

These entries were released as DDBJ daily updates on Oct. 20, 2009.

DAD (DDBJ amino acid database) Rel. 49.0 Released Oct. 14, 2009

ARSA database search (DDBJ, DAD) temporary unavailable Oct. 14, 2009
ARSA is a high-speed data retrieval system provided by DDBJ via WWW and Web API. DDBJ and DAD database search in ARSA is unavailable in the following schedule for update each of released data (DDBJ Release 79.0, DAD Release 49.0). Details are as follows:

  • Date & Time: Oct. 20, 2009 (Tue) 09:00 - 18:00 (We will announce on this page when the service resumes)
  • Unavailable services:
      DDBJ and DAD search in ARSA (another 18DBs are searchable. Search results do not contain DDBJ and DAD entries)
      ARSA reference function in TX Search
      DNA/Protein/AllDBs search at the search box of the upper part of DDBJ HP (another DB search are available)

Thank you for your understanding and cooperation.

Maintenance works finished. Thank you for your cooperation. (Oct. 20, 2009 at 17:15)

DDBJ Rel. 79 Completed Sep. 25, 2009

Change in the anonymous FTP site: Made a new directory "dra", renamed "trace" to "dta" Sep. 17, 2009
A new directory, "dra", was made under "ddbj_database" of DDBJ anonymous FTP site.
Now, all of released data from DDBJ Sequence Read Archive can be downloaded from the new "dra" directory.

"trace" directory was renamed to "dta", according to the official launch of DDBJ Trace Archive (DTA). For details of the change in "ddbj_database" directory and its subdirectories, see README.TXT in the
directory.
If you automatically monitor DDBJ anonymous FTP, please confirm your monitoring program if necessary.

Suspension of some parts of DDBJ activities during national holidays Sep. 11, 2009
DDBJ suspend our business of releasing data and answering all inquiries from September 19, 2009 to 23.
Search/Analysis, FTP, and all other WWW services are accessible. We will resume the normal business from September 24.

Thank you for your understanding and cooperation.

Change of directory structure of anonymous FTP site: Made a new directory "tpa" Aug. 28, 2009
A new directory, "tpa", was made under "ddbj_database" of DDBJ anonymous FTP site.
Before this change, TPA (Third-Party Annotaion) data were separated into three directories; "ddbj",
"ddbjnew" (for daily updates), and "wgs". Now, all of TPA associated data can be downloaded from
the new "tpa" directory.

For details of the change in "ddbj_database" directory and its subdirectories, see README.TXT in the
directory.
If you automatically monitor DDBJ anonymous FTP, please confirm your monitoring program if
necessary.

Redistribution of genomic sequence (build 4) of the cultivar Nipponbare of Japanese rice (Oryza sativa Japonica Group) assigned with RAP annotation Aug. 11, 2009
The entries corresponding to complete sequences of japonica rice chromosomes
were updated from build 3 to build 4.
Their accession numbers are AP008207-AP008218.
The updated contents were the results annotated by The Second Rice Annotation
Project Meeting (RAP2) which was an international rice genome annotation project
organized by Japanese research groups.
By this updating, AP008207-AP008218 entries were redistributed with
approximately 28,000 CDS (protein coding region) features.

The accession numbers  (Anonymous FTP)  are as follows ;
rice

Reference sites

(Photo: Integrated Database Project)

Request for the re-submission of the queries (Re: Homology Search and ClustalW temporary down (Aug.3)) Aug. 04, 2009
At first, DDBJ apologize the accidental suspension of DDBJ's Homology Search and ClustalW services which was broken out in the early morning of August 2, 2009.

After the investigation, some queries might not had returned the correct results because of the trouble of the target databases caused by the service suspension. Therefore, DDBJ asks the users who had submitted the queries during the following period to re-submit again. At present, DDBJ's Homology Search and ClustalW services works normally and returns the correct results.

  • period : Aug 2, 2009 around 6:00(JST) - Aug 3, 2009 17:40(JST)

Thank you for your cooperation and understanding.

(Urgent!)Homology Search and ClustalW temporary down Aug. 03, 2009
DDBJ's Homology Search and ClustalW services provided via WWW is currently unavailable since Aug. 2(Sun) 6:00(JST). At present, we are doing recovery efforts for the earliest resume. The resume will be notified on this DDBJ HP. Thank you for your understanding and cooperation.

The service was resumed. DDBJ awfully apologize for your inconvenience caused by the long time suspension (Aug. 3, 2009 at 17:40 JST)

Release of new tobacco (Nicotiana tabacum) EST 65,102 entries Jul. 24, 2009
tobacco
DDBJ newly released 65,102 entries of EST data derived from tobacco (Nicotiana tabacum), which had been submitted by Japan Tobacco Inc.

The accession numbers  (Anonymous FTP)  are as follows;

These entries were released as DDBJ daily updates on Jul. 23, 2009.

(Photo: Integrated Database Project)

ARSA DDBJ database search temporary unavailable Jul. 21, 2009
ARSA is a high-speed data retrieval system provided by DDBJ via WWW and Web API. DDBJ database search in ARSA is unavailable due to the system error. Details are as follows:

  • Date & Time: Jul. 19, 2009 (Sun) 9:58 -- (We will announce on this page when it resumes.)
  • Suspended services: DDBJ in ARSA
  • Note: Currently, ARSA is still available except for DDBJ database search.
    (another 19DBs are searchable. Search results do not contain DDBJ entries)

Thank you for your understanding and cooperation.

Maintenance works finished. Thank you for your cooperation. (Jul. 21, 2009 at 19:50 JST)

A new alignment service (MAFFT API) was opened to the public from WABI Jul. 16, 2009
MAFFT service was opened to the public in Web API for Biology (WABI). MAFFT is a fast and accurate multiple alignment program developed by Dr.
Kato of Kyushu university (http://align.bmr.kyushu-u.ac.jp/mafft/software/)

Enhancement of GIB-V by adding host information Jul. 16, 2009
Genome Information Broker for Viruses (GIB-V) extracted 52,088 complete virus genomes or segments data from DDBJ release 78 and enhanced host information. The host information which is not written in DDBJ entry is added by using cross reference information of UNIPROT entry. Furthermore, a common name is converted to a scientific name by using TxSearch system.

The paper about WABI was published in NAR Web server issue Jul. 16, 2009
The paper about Web API for Biology (WABI) was published in 2009 Web Server Issue of Nucleic Acids Research (Volume 37 Issue 12 July 2009).
"Web API for biology with a workflow navigation system"
Yeondae Kwon, Yasumasa Shigemoto, Yoshikazu Kuwana and Hideaki Sugawara
Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W11-W16

DAD (DDBJ amino acid database) Rel. 48.0 Released Jul. 14, 2009

ARSA database search (DDBJ, DAD) temporary unavailable Jul. 08, 2009
ARSA is a high-speed data retrieval system provided by DDBJ via WWW and Web API. DDBJ and DAD database search in ARSA is unavailable in the following schedule for update each of released data(DDBJ Release 76.0, DAD Release). Details are as follows:

  • Date & Time . Jul. 15, 2009 (Wed) 10:00 - 20:00 (We will announce on this page when the service resumes.):
  • Unavailable services:
      DDBJ and DAD search in ARSA (another 18DBs are searchable. Search results do not contain DDBJ and DAD entries)
      ARSA reference function in TX Search
      DNA/Protein/AllDBs search at the search box of the upper part of DDBJ HP.(another DB search are available)

Thank you for your understanding and cooperation.

Maintenance works finished. Thank you for your cooperation. (Jul. 15, 2009 at 20:00)

Homology Search and ClustalW temporary down Jul. 07, 2009
DDBJ's Homology Search and ClustalW services provided via WWW is temporarily unavailable in the following schedule for the system maintenance.

  • Date & Time. Jul. 13, 2009 (Mon) at 11:30 - 13:30 (JST) (We will announce on this page when it resumes.):
  • Unavailable services:
      - Homology search (FASTA, BLAST, PSI-BLAST, SSEARCH, HMMPFAM)
      - ClustalW

Thank you for your understanding and cooperation.

Maintenance works was finished. Thank you for your cooperation.(Jul. 13, 2009 at 14:00 JST)

DDBJ Rel. 78 Completed Jun. 23, 2009

Completion of a bug fixation: error in displaying suppressed entries by getentry Jun. 23, 2009
getentry is the entry retrieval system by accession numbers etc., which is provided by DDBJ via WWW and WebAPI.

The system had a trouble in displaying suppressed entries as of February, 2009; some search results were presented in incorrect output formats. This bug was fixed on Jun. 22, 2009.

Reference: Apology for the output format error in getentry Feb. 26, 2009

We apologize for your inconvenience and thank you for you cooperation.

GIB temporary down Jun. 10, 2009
GIB (Genome Information Broker) will be unavailable at the following schedule, because of the maintenance works.

  • Date: June 30(Tue), 2009 at 9:00(JST) - July 2(Thu) at 17:00 (JST)
Thank you very much for your understanding and cooperation.

Maintenance works finished, and the service is available. Thank you for your cooperation.(Jul. 1, 2009 at 14:45 JST)

Apology for the system failure of the Homology Search (Blast and Psi-Blast) Jun. 5, 2009
In the Blast and Psi-Blast of DDBJ Homology Search Services provided via WWW and WebAPI, the system did not work normally during the following period. The details are as follows:

  • Period: from June 2, 2009 at 20:32 (JST) to June 3, 2009 at 15:00 (JST)
  • Services: BLAST, PSI-BLAST
  • Databases: Protein default data(UniProt + PRF + PDB), Uniprot, Uniprot/TrEMBL
  • Condition: When the BLAST or PSI-BLAST search was executed specifying the above databases, the result was not shown in the web screen/result mail.
  • Cause: Existence of A large size data beyond the server setup limit

If you had submitted queries during the above period and did not obtain the correct results, please submit them again. We apologize for your inconvenience.

Release of new silkworm (Bombyx mori) small RNA MGA 4,448,218 entries Jun. 3, 2009
DDBJ newly released 4,448,218 entries of¡¡MGA data derived from silkworm (Bombyx mori), which had been submitted by University of Tokyo.

The accession numbers are as follows;

  • AHAAB0000001-AHAAB0547473
  • AHAAC0000001-AHAAC1704525
  • AHAAD0000001-AHAAD2196220
  • (total 4,448,218 entries)

Related site: About Mass sequence Genome for Sequence (MGA) entry
Anonymous FTP:
AH_resource_index

These entries were released as DDBJ daily updates on June 1, 2009.

Apology for the system failure of the Homology Search and ClustalW May 13, 2009
DDBJ provides Homology Search Services and ClustalW via WWW and WebAPI.

Because of the system failure, search and analysis had not been executed against the all queries during the following period. The details are as follows:
  • Period: from May 13, 2009 at 18:00 (JST) until around 22:20 (JST)
    At present, all services are resumed, and they works normally.
  • Services: FASTA, BLAST, PSI-BLAST, SSEARCH, HMMPFAM, ClustalW
  • Cause: System Failure
  • Among the queries which had been submitted to during the above period, some queries were accepted (Request IDs were issued) but unfortunately, there were some queries which were not accepted normally. The accepted queries are being executed their search and analysis. But, if you could not confirm your Request IDs when you submitted, we ask you to submit your queries again.
We apologize for your inconvenience and thank you for you cooperation.

Release of new Japanese common newt (Cynops pyrrhogaster) EST 25,600 entries May 1, 2009
nihon_imori
DDBJ newly released 25,600 entries of EST data derived from Japanese common newt (Cynops pyrrhogaster), which had been submitted by Kyoto University.

The accession numbers are as follows;

  • FS290155-FS315754 (25,600 entries)

These entries were released as DDBJ daily updates on April 25, 2009, and available by getentry or ARSA.

(Photo: provided by the submitter)

Update of databases related to the H-Invitational May 1, 2009
The mirror H-Invitational Database (H-InvDB) was upgraded on April 27, 2009. The latest version 6.2 of H-InvDB is now available.

Release of Swine Influenza A (H1N1) Virus Apr. 30, 2009
Release of Swine Influenza A (H1N1) Virus by DDBJ/EMBL/GenBank International Nucleotide Sequence Database.

The accession numbers (Anonymous FTP)  are as follows;(These entries are also available by getentry or ARSA)

Reference URLs:

Phylogenetic tree of HA (hemagglutinin) obtained from recent recent human cases of swine influenza A virus (H1N1) infections.
Click here.

Release of new chinese licorice (Glycyrrhiza uralensis) EST 50,594 entries Apr. 24, 2009
DDBJ newly released 50,594 entries of EST data derived from rhizomes of chinese licorice (Glycyrrhiza uralensis), which had been submitted by Chiba University.

The accession numbers  (Anonymous FTP)  are as follows;

These entries were released as DDBJ daily updates on April 24, 2009.

ARSA temporary down Apr. 15, 2009
ARSA is a high-speed data retrieval system provided by DDBJ via WWW and Web API. ARSA is unavailable in the following schedule for update each of released data (DDBJ Release 77.0, DAD Release 47.0) and server enhancement.

  • Date & Time. Apr. 21, 2009 (Tue) at 10:00 - Apr. 22, 2009 (Wed) at 18:00 (JST) (We will announce on this page when it resumes.):
  • Unavailable services:
      - ARSA
      - ARSA reference function in TX Search
      - DNA/Protein/AllDBs search at the search box of the upper part of DDBJ HP.

Thank you for your understanding and cooperation.

Maintenance works was finished. Thank you for your cooperation. (Apr. 22, 2009 at 16:40 JST)

Apology for error of Korean Patent data in the getentry Apr. 15, 2009
getentry is the entry retrieval system by accession numbers etc., which is provided by DDBJ via WWW and WebAPI.
In the getentry, during the following period, some incorrect Korean Patent entries were included. Details are as follows.
  • Database: "Patnet" in the Protein DATABASE
  • Accession Nos:4,541 entries of DI500718 - DI613550 (see the list)
  • Period: March 31 - April 8, 2009.
  • Cause: In the modification process of the previously released entries, wrong accession numbers were assigned to the corresponding patent numbers. As a result, the relation between the patent number and the accession numbers was not correct.
  • Measure: Any relevant data were already deleted, and will be re-released after the completion of the correction.
    The problem has been fixed. ( May. 1, 2009 )
We apologize confusing you very much.

DAD (DDBJ amino acid database) Rel. 47.0 Released Apr. 15, 2009

HMMPFAM temporary down Apr. 13, 2009
DDBJ provides HMMPFAM which is a motif search program against Pfam motif database on the basis of Hidden Markov Model (HMM).

For the urgent maintenance work, HMMPAM will be suspended as the following schedule.
  • Period: April 14, 2009 (Tuesday) 9:00 - 17:00 (JST)
Thank you for your understanding and cooperation.

Maintenance works finished, and the service is available. Thank you for your cooperation. (18:00)

NIG network service temporary down due to electric power outage. Apr. 13, 2009
NIG network service affected by the electric power outage because of substation trouble occurred on Apr. 12. Details are as follows:
  • Date: Apr. 12(Sun), 2009 around 5:00 (JST)
  • Affected service: NIG network service
  • Period when all services stopped : Apr. 12 (Sun) around 5:00 to Apr. 13 (Mon) 11:20(JST)
  • At present, all services are resumed. We apologize for your inconvenience.

    Release of rat GSS 227,486 entries Apr. 1, 2009
    DDBJ newly released rat (Rattus norvegicus LE/Stm) GSS 227,486 entries, which had been submitted by Kyoto University.

    Reference URL:
        http://www.anim.med.kyoto-u.ac.jp
    The accession numbers (Anonymous FTP) are as follows;

    These entries were released as DDBJ daily updates on April 1, 2009.

    DDBJ Rel. 77 Completed Mar.24, 2009

    Mirroring H-Invitational DB temporary down Mar. 19, 2009
    Mirroring H-Invitational DB will be unavailable at the following schedule,
    because of the maintenance works.

    • Date: March 31(The), 2009 at 9:00(JST) - April 1(Web) at 17:00 (JST)

    Thank you very much for your understanding and cooperation.

    The service was resumed (Apr. 1)

    Release of new tomato full length cDNA (HTC) data 10,959 entries and EST data 27,216 entries Mar. 19, 2009
    DDBJ newly released sequence data, tomato (Solanum lycopersicum) full length cDNA (HTC) 10,959 entries and EST 27,216 entries, which had been submitted by Kazusa DNA Research Institute.

    Reference URL:
        http://www.pgb.kazusa.or.jp/kaftom/

        http://www.kazusa.or.jp/jsol/microtom/indexe.html

    The accession numbers (Anonymous FTP)  are as follows;

    These entries were released as DDBJ daily updates on 3/19.
    Apology for the system failure of the Homology Search and ClustalW Mar. 13, 2009
    DDBJ provides Homology Search Services and ClustalW WWW and WebAPI.

    Because of the system failure, search and analysis had not been executed against the all queries during the following period. The details are as follows:
    • Period: from March 8, 2009 at 17:55 (JST) to March 9, 2009 at 09:08 (JST)
    • Services: FASTA, BLAST, PSI-BLAST, SSEARCH, HMMPFAM, ClustalW
    If you had submitted queries during the above period, please submit them again. We apologize for your inconvenience.

    NIG and DDBJ network services temporary down Mar. 5, 2009
    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: March 11(W), 2009 at 21:00 - 22:00 JST
      15 minutes interception during the above time

    Thank you very much for your understanding and cooperation.

    Release of new human CAGE MGA 7,824,360 entries Mar. 1, 2009
    DDBJ newly released MGA 7,824,360 entries derived from human acute monotypic leukemia cell line (THP-1) CAGE, which had been submitted by RIKEN.

    Reference URL: http://www.osc.riken.jp/
    The accession numbers are as follows;

    • AFAAA0000001-AFAAA0543260 (543,260 entries)
    • AFAAB0000001-AFAAB0191814 (191,814 entries)
    • AFAAC0000001-AFAAC0474745 (474,745 entries)
    • AFAAD0000001-AFAAD0353461 (353,461 entries)
    • AFAAE0000001-AFAAE0270208 (270,208 entries)
    • AFAAF0000001-AFAAF0513982 (513,982 entries)
    • AFAAG0000001-AFAAG0349448 (349,448 entries)
    • AFAAH0000001-AFAAH0425524 (425,524 entries)
    • AFAAI0000001-AFAAI0358861 (358,861 entries)
    • AFAAJ0000001-AFAAJ0285303 (285,303 entries)
    • AFAAK0000001-AFAAK0327328 (327,328 entries)
    • AFAAL0000001-AFAAL0456381 (456,381 entries)
    • AFAAM0000001-AFAAM0436519 (436,519 entries)
    • AFAAN0000001-AFAAN0499442 (499,442 entries)
    • AFAAO0000001-AFAAO0682996 (682,996 entries)
    • AFAAP0000001-AFAAP0716451 (716,451 entries)
    • AFAAQ0000001-AFAAQ0546880 (546,880 entries)
    • AFAAR0000001-AFAAR0391757 (391,757 entries)

    Related site: About Mass sequence Genome for Sequence (MGA) entry
    Anonymous FTP AF_resource_index:
    ftp://ftp.ddbj.nig.ac.jp/ddbj_database/mga/AF_resource_index.html

    These entries were released as DDBJ daily updates on February 27, 2009.

    Apology for the output format error in getentry Feb. 26, 2009
    getentry is the entry retrieval system by accession numbers etc., which is provided by DDBJ via WWW and WebAPI.
    At the suppress entries retrieval under the following conditions, the results are displayed in the format different from the specified format. The details are as follows:
    [Retrieval conditions]

    • database: DDBJ
    • output format: FASTA(incl. CDS), DDBJ-XML, INSD-XML
    • Result (how to obtain the result): E-mail, FTP

    [Phenomenon]
    In the sequence retrieval of the suppress entries under the above conditions, the corresponding suppress entries are outputted in the DDBJ flat file format, although the different format was specified.
    When the entries either do not fit the above conditions and/or are other than suppress entries, there are no problems.

    [Measure]
    At present, DDBJ works on this problem. We will inform at this DBJ HP as soon as the problem is fixed. Thank you for your understanding and cooperation.

    Apology for the system failure in HMMPFAM Feb. 20, 2009
    DDBJ provides HMMPFAM which is a motif search program against Pfam motif database on the basis of Hidden Markov Model (HMM).

    Because of the system failure, in DDBJ's HMMPFAM, queries had not been accepted normally during the following period. The details are as follows:

  • Period: from January 8, 2009 to February 14, 2009 at 02:52 (JST)
  • Condition:
      obtain results by WWW: no results were displayed even you click "view result" button.
      obtain results by E-mail: an empty mail was returned.
  • The bug was fixed already, and now, the results are available either by WWW or by E-mail. We apologize for your inconvenience for a long time.

    Mirroring H-Invitational DB temporary down Feb. 16, 2009
    Mirroring H-Invitational DB will be unavailable at the following schedule,
    because of the maintenance works.

    • Date: February 20(Fri), 2009 at 17:00(JST) - 23(Mon) at 12:00 (JST)

    Thank you very much for your understanding and cooperation.

    Apology for a part of the latest INSD data are not displayed in getentry and ARSA Feb. 06, 2009
    In the DDBJ/EMBL/GenBank International Nucleotide Sequence Database, owing to some accident, a part of EMBL originated entries were overwritten by the old data, and were incorporated into the search target database for getentry and ARSA.
    Therefore, since February 5 (Thu) early morning (JST), the entries of the listed accession numbers (see the list) are not displayed at the latest version (other than listed entries are correctly displayed).

    At present, DDBJ hastens to the recovery works of the latest version data (the works are scheduled to finish within February 6. Completion of the works will be notified in this DDBJ HP.)
    If you did a search of the DDBJ database using getentry and/or ARSA after February 5 (Thu) early morning (JST), please execute your search again after the completion of the data recovery.

    We awfully apologize for your inconvenience.

    Data recovery works are finished. Thank you for your cooperation.(Feb. 6, 2009 at 18:40(JST))

    Temporary suspension of DDBJ services for the system enhancement Jan. 28, 2009
    DDBJ temporarily suspends a part of DDBJ computer services at the following schedule, because of the computer system enhancement works.

    Service Period
    - SAKURA Feb. 17(Tue) 17:00(JST) - Feb. 18(Wed) 17:00(JST)
    - DDBJHP
    - getentry
    - TXSearch
    - ARSA
    - Homology Search (including ClustalW)
    - Vector Screening System
    Feb. 18 (Wed) 9:00 - 17:00(JST)
    The above is estimated schedule. Each service will be resumed as soon as the works are completed.
    We are sorry for your inconvenience, but we will appreciate for your understanding and cooperation.
    All services are resumed. Thank you for your cooperation. (Feb. 18, at 17:00 JST)

    Fix of the problem displaying CON entries in the getentry Jan. 16, 2009
    getentry is the entry retrieval system by accession numbers etc., which is provided by DDBJ via WWW and WebAPI.

    In June, 2008, in displaying the sequences of CON entries, 2 problems had happened.
    Details are as follows.
    Problems happened in June, 2008
    (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, whereas it should be processed into the complementary sequence (Fixed in Jul, 2008)
    (2) When the piece entry of retrieved CON entry contains a CON entry, it can not be processed correctly.
    Problems fixed in January, 2009
    (1) Contents of the problems
    In the getentry, to get the conjugated sequences of CON entries, two methods (display on browser and FTP) are provided. However, neither of two methods works properly in the case of retrieving CON entries under the following conditions.

    (2)Affected services: getentry, ARSA, Web API (GetEntry )
    (3)Measure completed date: January 13, 2009
    (4)Reference: Apology for the defective results of CON entries in getentry(June 20, 2008)

    We sincerely apologize for your long time inconvenience.

    DAD (DDBJ amino acid database) Rel. 46.0 Released Jan. 16, 2009
    • 13,526,116 entries:    3,599,816,846aa (total number of residues)
    • Changes in the present release:
          DDBJ/EMBL/GenBank Feature Table: Defin was revised in October, 2008
    • DAD Release Note
    • Latest Release Information

    ARSA database search (DDBJ, DAD) temporary unavailable Jan. 9, 2009
    ARSA is a high-speed data retrieval system provided by DDBJ via WWW and Web API. DDBJ and DAD database search in ARSA is unavailable in the following schedule for update each of released data (DDBJ Release 76.0, DAD Release). Details are as follows:

    • Date & Time. Jan. 16, 2009 (Fri) 9:00 - 18:00 (We will announce on this page when it resumes.):
    • Unavailable services:
        DDBJ and DAD search in ARSA (another 18DBs are searchable. Search results do not contain DDBJ and DAD entries)
        ARSA reference function in TX Search
        DNA/Protein/AllDBs search at the search box of the upper part of DDBJ HP.(another DB search are available)

    Thank you for your understanding and cooperation.

    Maintenance works finished. Thank you for your cooperation. (Jan. 16, 2009 at 18:30)

    Apology for the ARSA emergency suspension due to the system accident during the new-year holidays 2009.1.5
    ARSA is a high-speed data retrieval system provided by DDBJ via WWW and Web API.
    Because of the system trouble broken out on January 1, 2009 (unfortunately, it was during the new-year holidays), the ARSA service had been unavailable until today (Jan. 5 at 10:00). At present, the service is resumed. DDBJ apologize for your long-time inconvenience.

    PRF Release 124 released Dec.26, 2009

    DDBJ Rel. 76 Completed Dec.24, 2008
    ページの先頭へ戻る