Last updated:2014.12.5.

What’s New(2007)

DDBJ Rel. 72 Completed Dec. 25, 2007
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public. We completed DDBJ Release 72 in December 25, 2007. DDBJ Release 72 consists of 79,004,098 entries, and the number of bases reached 82,592,245,487.

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

As was already notified, DDBJ proceeded deletion of the both phone and fax numbers, and E-mail address from the flat files of the entries submitted to DDBJ. The retrofit of the all entries was completed by the issue of this release 72. Hereafter, database users become difficult to contact submitters based on the information described in the DDBJ flat files. When you wish to contact to the submitter(s) of an entry of your interest, please contact us using the prescribed inquiry form placed in the DDBJ HP.

Release of new Japanese macaque (Macaca fuscata) GSS 167,159 entries Dec. 19, 2007
DDBJ newly released Japanese macaque (Macaca fuscata) GSS 167,159 entries, which had been submitted by RIKEN Genomic Sciences Center. These entries were released as DDBJ daily updates on 12/18, and are available by anonymous FTP.

Release of new Monosiga ovata EST 69,143 entries and GSS 60,757 entries Dec. 19, 2007
DDBJ newly released Monosiga ovata EST 69,143 entries and GSS 60,757 entries, which had been submitted by RIKEN Genomic Sciences Center.
These entries were released as DDBJ daily updates on 12/18, , and are available by anonymous FTP.

The accession numbers and corresponding file names are as follows.

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

Mirroring H-Invitational DB temporary down due to the electric power cut in the NIG Dec. 19, 2007
Mirroring H-Invitational DB is temporary down due to the electric power cut of NIG, at the following schedule.

  • Date & Time:Dedcember 21(Fri), 2007 at 18:00(JST) - December 25(Tue) at 10:00(JST)

Resume of the service will be notified at this DDBJ HP. Thank you very much for your understanding and cooperation.

The service was resumed (Dec. 6, 2007 at 9:30 JST)

NIG network services temporary down Dec. 17, 2007
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:December 19(W), 2007 at 20:00 - December 20(Th) at 03:00 JST
    10 minutes interception during the above time
Thank you very much for your understanding and cooperation.

Mirroring H-Invitational DB temporary down for the unscheduled maintenance works Dec. 10, 2007
Mirroring H-Invitational DB is cureently unavailable because of the emergency maintenance works.
Resume of the service will be notified at this DDBJ HP. Thank you very much for your understanding and cooperation.

The service was resumed (Dec. 10 at 13:00 JST)

Coping with the RNA World -- The Revision of Feature Table Definition to Respond to the Demands of the Present Age -- Dec. 6, 2007
Researchers who use DDBJ may mainly concern with genomic sequences, mRNA transcripts and protein-coding genes. Of course some researchers focusing molecular taxonomy may also be interested in rRNA sequences. Is it sufficient for the sequence database to prepare 4 types of features for mRNA, CDS, rRNA and, source (the origin of the sequence), then ?

In fact, there are 62 feature keys that are officially defined by DDBJ/EMBL/GenBank in the Feature Table Definition Document (FT-Doc). This FT-Doc has been revised every April and October. Before the last revision in October 2007, there were 65 feature keys. It does not mean that we, DDBJ/EMBL/GenBank, abolished three old feature keys. We removed five old feature keys and created two new feature keys after very careful thinking. We do not only collect and provide sequence data submitted, but also make every effort to keep up with the progress of research and development in biology.
To discuss the revision of FT-Doc and some other issues, we have held the International Collaborators Meeting every year (ref: The Report for the 20th International Collaborators Meeting).

One of the major topics at the meeting this year (2007) was "How to describe the diverse RNA transcripts?". Recently, many new RNA transcripts (miRNA, siRNA, and so on) were found and elucidated. Before the revision of FT-Doc, such new RNA genes were described by using the old feature key, misc_RNA that meant "other RNA transcript". It was actually a tentative resort for a rapidly developing research area. We thought it was the time to reflect the fruit of the research to the definition of feature keys.

We, DDBJ/EMBL/GenBank, worked out the problem by addition of two RNA feature keys, ncRNA and tmRNA. The number of non-protein-coding RNA families is supposed to continue to increase, so, they will be classified into ncRNA feature. Also, three old feature keys, snRNA, snoRNA, and scRNA are merged into ncRNA by this month, December 2007. Some of old data with misc_RNA features will be modified with ncRNA or tmRNA, respectively.

We call such modifications as fitting legacy data to new rules "retrofit". Every year, we apply new feature rules to the data schema by October, and retrofit the data by December. The retrofit in December 2007 is symbolic of our struggle against a paradigm shift related to RNA world.

(The below is cited from "The Report for the 20th International Collaborators Meeting")


  • New ncRNA feature
    A variety of new types of RNA transcripts, "miRNA", "siRNA", and so on, have been introduced in recent years. Because the number of non protein coding RNA families is quite likely to continue to expand, a
    new ncRNA feature that can flexibly accommodate them will be introduced.

    Furthermore, snRNA, snoRNA, and scRNA features are merged into ncRNA feature by December 2007.

  • New /ncRNA_class qualifier

    The new feature, ncRNA, will utilize a new qualifier called /ncRNA_class, with a controlled vocabulary to indicate what type of non-protein-coding feature is being represented.

    Format: /ncRNA_class="<ncRNA_class_TYPE>"
    Example: /ncRNA_class="miRNA"

    <ncRNA_class_TYPE> should be selected from the following list;

    "antisense_RNA"   "autocatalytically_spliced_intron"   "telomerase_RNA"
    "hammerhead_ribozyme"   "RNase_P_RNA", "RNase_MRP_RNA"
    "guide_RNA" "rasiRNA" "scRNA"
    "siRNA" "miRNA" "piRNA"
    "snoRNA" "snRNA" "SRP_RNA"
    "vault_RNA" "Y_RNA", "other"


  • New tmRNA feature
    To support a class of RNA transcripts that have dual tRNA-like and mRNA-like behaviors, a new tmRNA feature will belegal. See tmRDB and tmRNA Website that provide some backgroundinformation about the tmRNAs.

  • New /tag_peptide qualifier
    To indicate the nucleotide region encoding the proteolysis tag
    peptide of tmRNA, a new qualifier, /tag_peptide, will be used for the
    tmRNA feature.

    Format: /tag_peptide=<base_range>
    Example: /tag_peptide=90..122

Suspension of the DDBJ activity during the New Year Holidays Dec. 6, 2007
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 4, 2008.

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 29, 2007 to January 3, 2008
SAKURA suspension: from December 27, 2007 at 17:00(JST) to January 4, 2008 at 10:00(JST)
data release suspension: from December 27, 2007 to January 4, 2008
Thank you very much for your understanding and cooperation.

We wish you a Happy New Year.

Mirroring H-Invitational DB temporary down Nov. 29, 2007
Mirroring H-Invitational DB will be unavailable at the following schedule, because of the maintenance works.
  • Date: December 3(Mon), 2007 at 9:00 - December 5(Wed), 2007 at 24:00 (JST)

Thank you very much for your understanding and cooperation.

The service was resumed (Dec. 6)

Apology for the delivery failure of the ClustalW results E-mail Nov. 14, 2007
In the ClustalW which DDBJ provides through WWW and E-mail, the result mail delivery trouble broke out. Details are as follows:


  • Service:ClustalW
  • Period:from 16:06 on November 6, 2007 to 11:49 on November 9, 2007
  • Condition:In the ClustalW, either in the WWW or in the E-mail, when the "E-mail" was selected as the method of receiving the analysis results, the result (E-mail) was not returned.

  • Cause:The E-mail program of the ClustalW was not active during the above period
  • Results:The analysis results were correct

After the start-up of the ClustalW E-mail program, the all cumulated mails were deliverd. Presently, ClustalW works normally.

We deeply apologize for any inconveniences that this may have caused to our users.

Apology for releasing of defective files of human gut metagenome WGS data from anonymous FTP November 12, 2007
In relation to the "new human gut metagenome WGS 353,805 entries" released by DDBJ on October 18, 2007, the thirteen files (BAAU.gz to BABG.gz), which were placed on /database/wgs/ or /database2/wgs/ directory
of anonymous FTP,
had a problem that the each entry was duplicated.
The files contain flatfiles for human gut metagenome WGS data.

We deeply apologize for inconveniences.
The problem has been resolved now.
Please retrieve the corrected files again if you have got
defective files during the period until Nov. 12, 2007, 12:30 PM.

  • Period: 2007.10.18 - 2007.11.12 12:30 PM

  • Details of the files:

    Name    Accession numbers
    BAAU.gz    BAAU01000001-BAAU01028900
    BAAV.gz    BAAV01000001-BAAV01036326
    BAAW.gz    BAAW01000001-BAAW01016539
    BAAX.gz    BAAX01000001-BAAX01036455
    BAAY.gz    BAAY01000001-BAAY01030198
    BAAZ.gz    BAAZ01000001-BAAZ01031237
    BABA.gz    BABA01000001-BABA01035177
    BABB.gz    BABB01000001-BABB01020226
    BABC.gz    BABC01000001-BABC01009958
    BABD.gz    BABD01000001-BABD01037296
    BABE.gz    BABE01000001-BABE01020532
    BABF.gz    BABF01000001-BABF01016164
    BABG.gz    BABG01000001-BABG01034797

Release of new human gut metagenome WGS data, 353,805 entries October 18, 2007

SuperSINET service temporary down Nov. 5, 2007
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.

  • 10 minutes interception during 20:00 to 22:00, Nov. 8(Thu), 2007 JST
Thank you very much for your understanding and cooperation.

Apology for the Blast system error Nov 5, 2007
In the Blast homology search service which DDBJ provide via WWW and by E-mail, an system error broke out during the following period. Details are as follows.

*Service: BLAST
*Period: November 5, 2007 11:09 - 11:49 (JST)
*Cconditions: The returned results were not correct
At present, the correct results were returned. We DDBJ ask the users who had executed the BLAST search during the above period to execute the same search again.

We sincerely apologize for this trouble.

NIG and DDBJ Network services temporary down Nov 2, 2007
NIG (National Institute of Genetics) network services including NIG supercomputer (supernig) will be unavailable at the following schedule because of the electric power cut.

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

Date & Time:From Nov.9 (FRI) 17:00 to Nov.10 (SAT) 24:00 (JST)

DDBJ services suspension schedule:

The all services are resumed (at 12:00 Nov.12).

Services Suspend Resume (scheduled)
SAKURA Nov.9 (Fri) 13:00 Nov.12 (Mon) 12:00
getentry, ARSA, SRS,
Homology Search System,
ClustalW, SQmatch,
TXSearch,
Vector Screening System,
GIB,
PDB Retriever, LIBRA-I,
Lib score,
Anonymous-FTP
Nov.9 (Fri) 16:00 Nov.12 (Mon) 12:00
Mirroring H-Inv DB Nov.9 (Fri) 17:00 Nov.12 (Mon) 11:00
DDBJ HP Nov.9 (Fri) 17:00 Nov.10 (Sat) 24:00
Thank you for your cooperation and understanding.

ARSA 2nd Enhancement Nov 2, 2007
DDBJ fruther upgraded ARSA (All-round Retrieval of Sequence and Annotation) is the high-speed keyword search system provided by DDBJ.

The features of ARSA are as follows:

  • ARSA provides one-stop query to 24 life science databases (30 million entries) including DDBJ International Nucleotide Sequence Database.

  • ARSA will return a quick response to any query regardless of the complexity of the query, the number of hits to the query and the target database(s)

  • In the case of DDBJ, you can define search conditions in details by use of any combination of Features/Qualifiers of the DDBJ flat file.

  • Application Programming Interface (API) is prepared so that you can call some functions of ARSA from your programs such as Java, in your computer.

DDBJ added the following new functions this time.

  • Addition of the KEGG/PATHWAY database to the searchable databases
    KEGG/PATHWAY database was newly added. You can view the PATHWAY maps by clicking the PATHWAY IDs in the result lists.
  • Specification of detailed search conditions in the all databases, as well as DDBJ
    The detailed search conditions can be specified in the all databases (When you use this function, select the database in the top page, then click the "Cross Search" button).

  • Cross Search of multiple databases using the common search conditions
    When you select the multiple databases, you can use the above function by using the common search conditions (Check the multiple databases you would like to search in the top page, then click the "Cross Search" button).
Other improvements:

  • "&(AND)" and/or "|(OR)" can be entered into the search boxes directly
    (e.g. see the "Help" page)

  • The restriction for using the following words in the refine search was removed.
    (In the new ARSA, " ' ", " ( ", " ) ", " { ", " } " can be used as the search keywords)

arsatop
ARSA New Top Page
arsatop
Hit Count List Page
ARSA will continue to be enhanced, if you make comments. So, please visit ARSA and click "Your Comment" to help us to improve ARSA to help you.

Change of the sequence search system linked with TXSearch Oct 30, 2007
TXSearch is a retrieval system for a Taxonomy Database which was unified by DDBJ, GenBank and EMBL, which is developed by DDBJ. This should be helpful as a reference of taxonomic names when you submit nucleotide sequences to DDBJ.

Currently, TXsearch links to SRS which retrieves the related sequences, using the organism names, taxonomic names or ID numbers obtained by the TXsearch results. DDBJ changes this linked search system from SRS to ARSA (All-round Retrieval of Sequence and Annotation) according to the following schedule.
    Date: November 2, 2007 (Fri)
    (The changing works are scheduled in the afternoon, and the service does not suspend because of this works)

You can obtain the related entries information more rapidly with this change.

Apology for the undisplayable entries at the getentry Oct 22, 2007
getentry is the data retrieval system provided by
DDBJ through web and E-mail.

Recently, we found there were some entries, which had not been displayed at the getentry for a certain period. Details are as follows;

  • Affected periods: February 1, 2007 - September 13, 2007
  • Undisplayable entries:(-->see the accession numbers list)
  • Measures:The undisplayed data had been modified on September 13, 2007, and currently, all the data can be displayed.

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.

Update of databases related to the H-Invitational Oct 18, 2007
The mirror H-Invitational Database (H-InvDB) was upgraded on October 18, 2007. The latest version 4.6 of H-InvDB is now available.

Release of new human gut metagenome WGS data, 353,805 entries Oct 18, 2007
DDBJ newly released human gut microbiota metagenome WGS data, 353,805 entries, which had been submitted by University of Tokyo, Nara Institute Science and Technology, University of Miyazaki, University of Tokushima, Japan Agency for Marine-Earth Science and Technology, Azabu University, Kitasato University, Mitsubishi Research Institute INC. and RIKEN Genomic Sciences Center.

The results of of the human gut metagenomic research are introduced
in the following paper.

The accession numbers are as follows;

BAAU01000001-BAAU01028900 (28900 entries) (BAAU.gz)
BAAV01000001-BAAV01036326 (36326 entries) (BAAV.gz)
BAAW01000001-BAAW01016539 (16539 entries) (BAAW.gz)
BAAX01000001-BAAX01036455 (36455 entries) (BAAX.gz)
BAAY01000001-BAAY01030198 (30198 entries) (BAAY.gz)
BAAZ01000001-BAAZ01031237 (31237 entries) (BAAZ.gz)
BABA01000001-BABA01035177 (35177 entries) (BABA.gz)
BABB01000001-BABB01020226 (20226 entries) (BABB.gz)
BABC01000001-BABC01009958 ( 9958 entries) (BABC.gz)
BABD01000001-BABD01037296 (37296 entries) (BABD.gz)
BABE01000001-BABE01020532 (20532 entries) (BABE.gz)
BABF01000001-BABF01016164 (16164 entries) (BABF.gz)
BABG01000001-BABG01034797 (34797 entries) (BABG.gz)
These entries were released as DDBJ daily updates on October 18, 2007, and are available by anonymous FTP

Related Links:

Apology for releasing of defective files of human gut metagenome WGS data from anonymous FTP November 12, 2007

DAD rel. 41.0 was released Oct 12, 2007
DDBJ amino acid database (DAD) Release36 was released on Oct. 12, 2007 at DDBJ. DAD Release 41.0 consists of 11,364,503 entries, and the total number of residues reached 2,882,657,043.

FTP site for DB download

DDBJ HP Design Renewal Oct. 5, 2007

We updated our home page on October 5, 2007, to make our data submitters and users comfortable at the DDBJ site.
The key points of the updating are as follows:

  • Redesign of our site navigation system.

    Based on a current trend of web site design,

    • we have placed a global menu near the top of the page, and
    • local (context-sensitive) menus at the left- hand side of each page.
      Furthermore,

    • the bread-crumb trail is located under the
      left corner of the global menu to help you avoid losing your way in
      our web site.

    In the new HP when you click one of the global menus, you can observe all the contents of each service at a glance, and make the best choice without stress.

  • Creation of a window for searching databases at the top of each page:

    In the new HP, you can search following types of data from the search
    window of each page
    , without migrating to the main page of the
    databases here and there.


i) accession numbers (by getentry)
ii) keywords in DDBJ release and daily update (by SRS)
iii) keywords in Protein databases (by SRS)
iv) Scientific names and names of taxa (by TXSearch)
v) Full text search in the DDBJ site.

We will replace the keyword search engine of SRS with ARSA when a new version of
ARSA is ready. It will be in a couple of months.

NIG Network service temporary down Oct. 4, 2007
NIG (National Institute of Genetics) network service will be unavailable at the following schedule,
because of the network maintenance works.
All DDBJ network services and NIG supercomputer (supernig) service will also be unavailable.

Date & Time:October 5 (Fri) from 18:00 to 20:00

Thank you very much for your understanding and cooperation.

Maintenance works finished, and the services are resumed. Thank you for your cooperation.(20:00)

ARSA service suspension for 2 days Oct. 3, 2007
ARSA (All-round Retrieval of Sequence and Annotation) is the high-speed keyword search system provided by DDBJ.

Because of the further system upgrade works and periodical maintenance works, ARSA service will be unavailable at the following schedule. During this period, please use SRS and getentry as the substitute.

Suspension Date & Time: October 25(Thu) 9:00 - 26(Fri) 21:00 (Resume will be notified on this DDBJ HP)

Main improvements:

- Addition of the "PATHWAY" database to the searchable databases

- Specification of detailed search conditions is available in the all databases, as well as DDBJ

- Retrieval of multiple databases using the common search conditions is available

- Modification of the interface according to the above changes
Other improvements:

- Removal of the limit for the search keywords in the refine search
   (In the new ARSA, " ' ", " ( ", " ) ", " { ", " } " can be used)

- "AND" and/or "OR" should be entered into the search boxes directly

- Incompatibility of the "Search History" function
   (There are no compatibility of the search history between the current ARSA and the new ARSA)
We apologize for your inconvenience. Thank you for your understanding and cooperation.

The service was resumed. Please try the upgraded ARSA. Thank you for your cooperation. (at 20:00, October 26)

PRF Rel. 117 was released Oct. 2, 2007
PRF (Protein Research Foundation)/SEQ database Release 116 was released on
Sep. 28, 2007 at DDBJ. PRF Release 117 consists of 856,684 entries,
and the total number of residues reached 288,916,010.

DDBJ Rel. 71 Completed Sep. 27, 2007
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public. We completed DDBJ Release 71 in September 27, 2007. DDBJ Release 71 consists of 76,273,34 entries, and the number of bases reached 79,706,204,461.

FTP site for periodical release and new data download

As was already notified at DDBJ HP, DDBJ will delete both phone and fax numbers, and E-mail address from the flat files of the entries submitted to DDBJ. DDBJ plans to retorofit the entries submitted to DDBJ, not to GenBank or EMBL, by periodical release 72, the end of December 2007. For the details of this DDBJ flat file format revision, please see here.

Release of Silkworm GSS 94,904 entries Sep. 20, 2007
DDBJ released silkworm (Bombyx mori) GSS 94,904 entries, which had been submitted by National Institute of Agrobiological Sciences. These entries were released as DDBJ daily update on 9/14.

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

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

  • DE283657-DE378560¡Ê94,904 entries)

  • anonymousFTP file name:
    Bombyx_mori_GSS_070914_1.seq.gz

Apology for the ClustalW results error Sep. 18, 2007
DDBJ provides ClustalW services through WWW and E-mail. In the ClustalW results received by E-mails, incorrect results may have been returneed. Details are as follows:


  • Service:ClustalW
  • Period:from 14:00 on August 27, 2007 to 18:00 on September 7, 2007
  • Condition:When you selected "E-mail" to obtain the results and specified "AUTOMATIC" in the TYPE option (In the WWW, the default was selected. And in the E-mail server, "is_align 1" was specified without specifying DNA/PROTEIN in the type option), incorrect results might have been returned.
  • Cause:system error
  • Results:In the above cases, incorrect results might have been returned. Therefore, if you did the ClustalW analysis in the corresponding conditions during the above period, we are sorry but we ask you to do the analysis again in the same conditions to get the correct results (The program error had already been fixed, and now, the correct results can be obtained).

We deeply apologize for any inconveniences that this may have caused to our users.

getentry suspension for the maintenance Sep. 18, 2007
getentry is a data retrieval system provided by
DDBJ through web and E-mail.

For the regular maintenance work, getentry will be suspended as the following schedule.
  • September 27, 2007 (Thursday) 18:00 - 19:00

Note:In another DDBJ services such as ARSA, Homology Search (FASTA, BLAST, PSI-BLAST, SSEARCH) and SQmatch, viewing the result entries (invoked by the getentry program) is impossible during the suspension period(You can execute the retrieval).

Thank you for your understanding and cooperation.

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

getentry suspension for the maintenance Sep. 12, 2007
getentry is a data retrieval system provided by
DDBJ through web and E-mail.

For the urgentmaintenance work, getentry will be suspended today.
  • September 12, 2007 (Wednesday) 17:00 - 18:00

Note:In another DDBJ services such as ARSA, Homology Search (FASTA, BLAST, PSI-BLAST, SSEARCH) and SQmatch, viewing the result entries (invoked by the getentry program) is impossible during the suspension period(You can execute the retrieval).

Thank you for your understanding and cooperation.

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

Suspension of "H-Invitational Database CIB-DDBJ Flat File server" for system maintenance Sep. 12, 2007
H-Invitational Database CIB-DDBJ Flat File server(the database of full-length cDNAs assigned functional annotation as a result of H-Invitational in flat file compatible with the DDBJ flat file format) is unavailable for a while because of the system maintenance. Resume will be notified on this DDBJ HP.

Thank you very much for your understanding and cooperation.

DDBJ started new web service "REST"Sept. 7, 2007
DDBJ has opened to the public REST(Representational State Transfer)* service as a WEB service which is available from a program since August 2007. You can use it from XML Central of DDBJ. It is possible to integrate various systems such as search system, analysis program and data retrieve provided by DDBJ by using REST service. DDBJ opened to the public SOAP service as a service which can be available from program. However REST service has advantages compared to SOAP service as follows.

  1. REST is easy to use.
    Only you have to do is to input the URL in the web browser for accessing REST service. Furthermore we make sure that various program languages such as Perl, Java, C, Ruby and Python can be used in the case of using from a program. And you can also use REST services by using telnet or wget command.

  2. REST is easy to treat large-scale data.
    REST service provides you with the result as a stream. Therefore you can retrieve the result every one line and lower the machine load since it isn't saved to the computer memory. So you can retrieve large-scale data effectively by using REST service compared to SOAP. For example if you want to get a DDBJ genome data of Escherichia coli with flat file format, REST service provides you with more than three times speed compared to SOAP.

On the other hand, SOAP service has also advantages that coding volume is small and it has extensibility.
DDBJ will enhance WEB API(Application Program Interface) in the future to be more easy to use. Please contact xml-admin@ddbj.nig.ac.jp, if you have any opinions or suggestions.
* What is REST?

Apology for not shown alignment scores in ClustalW results Aug. 22, 2007
DDBJ provides ClustalW services through WWW and E-mail. There was a problem in viewing the results. Details are as follows:


  • Service:ClustalW
  • Period:from February 27, 2007 to August 7, 2007 18:00
  • Condition:When the "E-mail" is specified to obtain the results, "SHOW ALIGNMENT SCORE" and "SHOW SEQNO_RANGE SCORE" options were not active in spite of these options were specified. And accordingly, the Alignment scores were not included in the obtained results.
  • Cause:program error
  • Results:Fortunately, the results themselves were correct.

The program error had already been fixed, and now, the alignment scores are displayed in the results.
We deeply apologize for any inconveniences that this may have caused to our users.

Great increase of the number of CON entries in DDBJ Rel.70: huge scale metagenome data Aug. 21, 2007
Total number of CON entris greatly increased from 983,699 to 3,932,751 in the latest DDBJ release (DDBJ Rel.70).
This big growth is caused by the addition of 4,087,206 entries, submitted from J. Craig Venter Institute, in 2007 April released so far.

The data are the results of marine metagenomic research, and details are introduced in the following papers.

Also, please visit the project web page;

The entries are available on getentry, a retrieval tool of DDBJ (The data are available from the Anonymous FTP of the DDBJ" page (DDBJ Release and WGS). Accession numbers of the entries are listed below.

      CON entries:    EM000001-EM999999,
EN000001-EN999999,
EP000001-EP999999,
EQ000001-EQ087209
Piece WGS entries:    AACY020000001-AACY024124495

NIG network service temporary down due to electric power interruption Aug. 20, 2007
NIG network service affectd by the electric power interruption which had occured on Aug. 20. Details are as follows:

    Period: Aug. 20 (Mon) 00:54 - 01:23

    Affectd service: NIG network service

   &nbspServices still unavailable

  • getentry
  • ARSA
  • FASTA, BLAST, PSI-BLAST, SSEARCH, HMMPFAM, CLUSTALW
  • Anonymous FTP
  • SQmatch
  • supernig
  • H-Invitational Database CIB-DDBJ Flat File Server, mirrorring H-InvDB

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

All services except homology search (FASTA, BLAST, PSI-BLAST, SSEARCH, HMMPFAM) and ClustalW are resumed. We apology for your inconvenience (As of Aug. 20 14:00).
Now the service works normally. We apologize for your inconvenience.

All services are resumed at 10:30 on Aug.21, and at present, the all service works normally. Sorry for your inconvenience ( Aug. 21 10:30).

Update of "Conference on Information Biology" Aug. 16, 2007
Following conferences were added to "Conference on Information Biology"

    2007

  • The 7th International Workshop on Advanced Genomics (11/27-28)

PRF Rel. 116 was released Aug. 13, 2007
PRF (Protein Research Foundation)/SEQ database Release 116 was released on
Aug. 8, 2007 at DDBJ. PRF Release 109 consists of 832,123 entries,
and the total number of residues reached 281,311,678.

Apology for the missing of TPA and CON INSD-XML data corresponding to the DDBJ Rel.70.1 in the anonymous FTP and ARSA
Aug. 10, 2007
TPA and CON data were missed from the Anonymous FTP of INSD-XML corresponding to the DDBJ release 70.1. Also, the data were not available on the ARSA.


  • INSD-XML formatted CON: 3,932,751 entries, approx.61GB (including "marine metagenome")
  • INSD-XML formatted TPA: 5,442 entries, approx.74MB
    [note]INSD-XML CON of DDBJ Rel.69 is 983,699 entries, approx.11GB

Anonymous FTP

At present, the correct data are available from the following FTP site. Therefore, if you had downloaded the INSD-XML formatted release data of DDBJ Release 70.1 during the following period, please make up the missing files(listed in the below).

  • Period: June 29, 2007 - August 10, 2007
  • Current directory: ftp://ftp.ddbj.nig.ac.jp/ddbj_database/ddbj/xml/insdxml_current/

  • files newly placed:

    ddbjcon1.insd_xml.gz,  ddbjcon2.insd_xml.gz,  ddbjcon3.insd_xml.gz,
    ddbjcon4.insd_xml.gz,  ddbjcon5.insd_xml.gz,  ddbjcon6.insd_xml.gz,
    ddbjcon7.insd_xml.gz,  ddbjcon8.insd_xml.gz,  ddbjcon9.insd_xml.gz,
    ddbjcon10.insd_xml.gz, ddbjcon11.insd_xml.gz, ddbjcon12.insd_xml.gz,
    ddbjcon13.insd_xml.gz, ddbjcon14.insd_xml.gz, ddbjcon15.insd_xml.gz,
    ddbjcon16.insd_xml.gz, ddbjcon17.insd_xml.gz, ddbjcon18.insd_xml.gz,
    ddbjcon19.insd_xml.gz, ddbjcon20.insd_xml.gz, ddbjcon21.insd_xml.gz,
    ddbjcon22.insd_xml.gz, ddbjcon23.insd_xml.gz, ddbjcon24.insd_xml.gz,
    ddbjcon25.insd_xml.gz, ddbjcon26.insd_xml.gz, ddbjcon27.insd_xml.gz,
    ddbjcon28.insd_xml.gz, ddbjcon29.insd_xml.gz, ddbjcon30.insd_xml.gz,
    ddbjcon31.insd_xml.gz, ddbjcon32.insd_xml.gz, ddbjcon33.insd_xml.gz,
    ddbjcon34.insd_xml.gz, ddbjcon35.insd_xml.gz, ddbjcon36.insd_xml.gz,
    ddbjcon37.insd_xml.gz, ddbjcon38.insd_xml.gz, ddbjcon39.insd_xml.gz,
    ddbjcon40.insd_xml.gz, ddbjcon41.insd_xml.gz, ddbjtpa.insd_xml.gz
    

ARSA search

Since the data addition to ARSA is still underway, so all of the CON and TPA data are not available on the ARSA. Please note that it would be likely to get incorrect results for DDBJ data. The completion of the data addition will be notified in this DDBJ HP.

As the data addition to the ARSA was completed, the correct results are available now (August 16, 18:00).

We apologize very much for your inconvenience, and appreciate your cooperation and understanding.

Update of the databases related to the H-Invitational Aug. 8, 2007
The contents of the databases related to the H-Invitational were updated. The main contents of the update are the following.

  • The number of cDNA (HIT; H-Invitational transcript) entry has changed from 175,542 to 175,536.
  • The number of LOCUS (HIX; H-Invitational cluster) entry has changed from 34,701 to 34,699.
  • The version of our mirror H-Invitational Database (H-InvDB) was upgraded from "4.0" to "4.3".

[Databases related to the H-Invitational project]

NIG Network service temporary down Aug. 8, 2007
NIG (National Institute of Genetics) network service will be unavailable at the following schedule,
because of the emergency network maintenance.
All DDBJ network services and NIG supercomputer (supernig) service will also be unavailable.

Date & Time:August 7 (Tue) from 18:00 to 21:00

Thank you very much for your understanding and cooperation.

Maintenance works finished, and the services are resumed. Thank you for your cooperation.(21:00)

ARSA was upgraded Aug. 3, 2007
DDBJ completed the trial service of ARSA and released it officially.

The features of ARSA are as follows:


  • ARSA provides one-stop query to 23 life science databases including DDBJ International Nucleotide Sequence Database.

  • ARSA will return a quick response to any query regardless of the complexity of the query, the number of hits to the query and the target database(s)

  • In the case of DDBJ, you can define search conditions in details by use of any combination of Features/Qualifiers of the DDBJ flat file.

  • Application Programming Interface (API) is prepared so that you can call some functions of ARSA from your Java or Perl programs in your computer.

DDBJ added the following new functions based on the users' comments.

  • The search results can be downloaded across databases (1)
  • The database can be selected in the reslut pages (3)
  • The result items shown in the result pages can be
    specified in the all databases (2, 4)
  • The number of the records per page can be changed (5)
  • The links of page jump are added in the result pages.
ARSA

Another Changes

  • The extension of file which can be downloaded with TSV format was changed from ".csv" to ".txt".
  • "Narrow Search " changed its name to "Refine Search".
  • SimpleQuery was removed.
  • HTTP download was abolished. You can download the results from anonymous FTP.

ARSA will continue to be enhanced, if you make comments. So, please visit ARSA and click "Your Comment" to help us to improve ARSA to help you.

(*) ARSA means "Here you go" in Japanese.

The Web page of "XML Central of DDBJ" is getting cool Aug. 3, 2007
xml-web
XML Central of DDBJ provides API (Application programming interface) in the framework of Web services based on SOAP (Simple Object Access Protocol).

Almost all the services that you have used with Web browsers are accessible by Java and Perl programs.
You can set up a workflow that mechanically processes your request while you take a coffee/tea break.

[Caution] Revision of DDBJ flat file format: Deletion of E-mail address, phone and fax numbers Aug. 1, 2007
Outline of revision
To follow the Japanese law of protecting personal information, DDBJ will delete both phone and fax numbers, and E-mail address from the flat files of the entries submitted to DDBJ. It would be also helpful to protect the DDBJ releases against SPAM mail senders. DDBJ plans to retorofit the entries submitted to DDBJ, not to GenBank or EMBL, by periodical release 72, the end of December 2007.

Up to now, database users can contact to sequence submitters by using their E-mail addresses on the DDBJ flat files. However, after this revision, it will become difficult to contact submitters. When you wish to contact to the submitter(s) of an entry of your interest, please contact us with the inquiry form with reasons briefly; i.e. asking to transfer cloned sequences, etc, then we will forward your messeage to the submitter(s).

Thank you very much for your understanding and cooperation.

Detailed particulars of revision
Now, the submitter information is described in JOURNAL line at REFERENCE 1 as,



  
  JOURNAL   Submitted (30-NOV-2000) to the DDBJ/EMBL/GenBank databases.
            Hanako Mishima, National Institute of Genetics, DNA Data
            Bank of Japan; Yata 1111, Mishima, Shizuoka 411-8540, Japan
            (E-mail:mishima@supernig.nig.ac.jp, Tel:81-55-981-6853,
             Fax:81-55-981-6849)


After the deletion or the information in question, DDBJ flat file will be
either one of the following two types;

Type 1: Phone and fax numbers and E-mail address are deleted.

  
  JOURNAL   Submitted (30-NOV-2000) to the DDBJ/EMBL/GenBank databases.
            Contact:Hanako Mishima
            National Institute of Genetics, DNA Data Bank of Japan; Yata 1111,
            Mishima, Shizuoka 411-8540, Japan

 
Type 2: When the submitters wish to keep their contact information disclosed,
it will be described as,


  JOURNAL   Submitted (30-NOV-2000) to the DDBJ/EMBL/GenBank databases.
            Contact:Hanako Mishima
            National Institute of Genetics, DNA Data Bank of Japan; Yata 1111,
            Mishima, Shizuoka 411-8540, Japan
            E-mail :mishima@supernig.nig.ac.jp
            Phone  :81-55-981-6853
            Fax    :81-55-981-6849


In principle, we will delete all of the items, "phone number", "fax number", and "E-mail address" from the entries that have been submitted to DDBJ as shown in "Type 1". However, if you wish to disclose any of the three items, please contact us at   , specifying the item(s) to be disclosed.

getentry suspension for the maintenance Jul. 31, 2007
getentry is a data retrieval system provided byDDBJ through web and E-mail.
For the maintenance work, getentry will be suspended on the following day.
  • August 8, 2007 (Wednesday) 17:00 - 18:00

Note:In another DDBJ services such as
Homology Search (FASTA, BLAST, PSI-BLAST, SSEARCH) and SQmatch, viewing the result entries (invoked by the getentry program) is impossible during the suspension period(You can execute the retrieval).

Thank you for your understanding and cooperation.

Maintenance works finished. Thank you for your cooperation.(18:00)

ARSA database search (DDBJ, DAD) temporary unavailable Jul. 30, 2007
ARSA is a high-speed data retrieval system provided by DDBJ through WWW. At the following schedule, DDBJ and DAD database search is unavailable for the database update. Details are as follows:

  • Date & Time: August 8, 2007(Wed) 9:00 - 18:00 (resume will be notified on this DDBJ HP)
  • Suspended services: DDBJ and DAD search in ARSA
  • Note: During the above period, ARSA is still available except for the above 2 databases search. If you would like to hasten to the search of the above 2 databases, please substitute SRS.

Thank you for your understanding and cooperation.

Maintenance works finished. Thank you for your cooperation.(18:00)

Release of new cricket (Gryllus bimaculatus) cDNA 32,010 entries Jul.27, 2007

DDBJ newly released two-spotted cricket (Gryllus bimaculatus) high throughput cDNA 32,010 entries, which had been submitted by University of Tokushima. These entries were released as DDBJ daily updates on July 26.
The accession numbers are as follows;

DDBJ release 70.1 as a revision of 70.0 Jul.24, 2007
DDBJ released DDBJ release 70.1 as a revision of 70.0 on July 24, 2007,
because some incorrect formatted data were contained in the release 70.

Revised version: DDBJ release 70.1 (released on July 24, 2007)
Original release: DDBJ release 70 (released on June 29, 2007)
Incorrect format line: Feature Table format
Corrected Acc Nos. : 53 entries
     AJ570278, AJ570279, AJ570280, AJ570281, AJ570283,
     AJ570284, AJ570285, AJ570286, AJ570287, AJ570288,
     AJ570289, AJ570290, AJ570291, AJ570292, AJ570294,
     AJ570295, AJ570296, AJ570297, AJ570298, AJ570299,
     AJ570300, AJ570301, AJ570302, AJ570303, AJ570305,
     AJ570468, AJ570470, AJ570471, AJ570472, AJ570473,
     AJ570474, AJ570475, AJ570476, AJ570477, AJ570478,
     AJ570479 AJ570481 AJ570482, td> AJ570483, AJ570484,
     AJ570485, AJ570486, AJ570487, AJ570488, AJ570489,
     AJ570490, AJ570492, AJ570493, AJ570494, AJ570495,
     X06674, X06675, AJ965256,    
Corrected files: ddbjbct1.seq
  ddbjhum5.seq
  ddbjinv1.seq
Reference: FTP site for periodical release and new data download

We DDBJ regret our mistake.

DAD rel. 40 was released Jul. 24, 2007
DDBJ amino acid database (DAD) Release40 was released on Jul. 24, 2007 at DDBJ. DAD Release 40 consists of 10,900,421 entries, and the total number of residues reached 2,729,493,910. Since this release, the CON division data has been included.

FTP site for DB download

Update of "Conference on Information Biology" Jul. 3, 2007

DDBJ Rel. 70 Completed Jul. 2, 2007
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public. We completed DDBJ Release 70 in June 29, 2007.
DDBJ Release 70 consists of 72,801,679 entries, and the number of bases reached 76,788,510,646.

FTP site for periodical release and new data download

Apology for the undisplayable WGS entries at getentry Jun. 22, 2007
getentry is the data retrieval system provided by DDBJ through web and E-mail.

Recently, we found there were some entries, which had not been displayed at the getentry for a certain period. Details are as follows;

The undisplayed data had been modified at the getentry maintenance works executed on June 19, 2007, and currently, all the data can be displayed.

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.

Restarting and update of the databases related to the H-Invitational Jun. 19, 2007
As a maintenance of the database service was completely finished, the mirror H-InvDB is now available.

The contents of the databases related to the H-Invitational was also updated at this time. The main contents of the update are the following.

  • The number of cDNA entry has increased 175,542 from 167,992
  • The number of LOCUS entry has changed to 34,701 from 35,005
  • Version of mirror H-Invitational Database (H-InvDB) upgraded to "4.0".

[Databases related to the H-Invitational project]

getentry suspension for the maintenance Jun. 11, 2007
getentry is the data retrieval system provided by
DDBJ through web and E-mail.

For the maintenance work, getentry will be suspended on the following day.
  • June 19, 2007 (Tuesday) 18:00 - 19:00

Note:In another DDBJ services such as ARSA, Homology Search (FASTA, BLAST, PSI-BLAST, SSEARCH) and SQmatch, viewing the result entries (invocated by getentry program) during the suspension period(You can execute the retrieval).

Thank you for your understanding and cooperation.

ARSA service suspension for 3 days Jun. 5, 2007
ARSA (All-round Retrieval of Sequence and Annotation) is the high-speed keyword search system provided by DDBJ.

Because of the system upgrade, ARSA service will be unavailable at the following schedule. During this period, please use SRS and getentry as the substitute.

Date & Time: June 20(Wed)9:00 - June 22(Fri)18:00

Note:The following functions will be improved after this upgrading suspension.

- downloadable all search results of multiple databases

- re-selectable the databases in the results screen

- re-selectable the numbers of the viewed results in the results screen

- add the page jump functions in the result screen

- change the extensions of CSV dowload files (.csv -> .txt)*

- Rename "Narrowsearch" to "RefineSearch"

- Stop SimpleQuery retrieval

- Stop download by HTTP
* Currently, in the CSV formatted download files, ".csv" extensions are attached, although the actual format is the tab-deliminated. Therefore, the extensions are changed to match the actual format type.

We apology for your inconvenience. Thank you for your understanding and cooperation.

The service was resumed. Please try the upgraded ARSA. Thank you for your cooperation. (at 18:00, June 22)
PRF Rel. 115 was released June 5, 2007
PRF (Protein Research Foundation)/SEQ database Release 115 was released on June 5, 2007 at DDBJ.
PRF Release 115 consists of 810,251 entries, and the total number of residues reached 274,842,827.

NIG Network service temporary down June. 4, 2007
NIG (National Institute of Genetics) network service will be unavailable at the following schedule,
because of the planned urgent network maintenance.
All DDBJ network services and NIG supercomputer (supernig) service will also be unavailable.

Date & Time:June. 7 (THU) from 14:00 to 17:00

Thank you very much for your understanding and cooperation.

SRS services suspended for the emrgency maintenanceJune. 1, 2007
SRS (Sequence Retrieval System) is the keyword retrieval service provided by DDBJ WWW server. Due to the hardware accident, the service was intercepted today (June 1, 2007 15:20 - 15:50). Because of this accident, unscheduled maintenance works is being executed from 17:00. If you would like to hasten to the keyword retreival, please substitute ARSA for SRS. Resume will be notified in thie page as soon as the trouble was resolved.
We apology for your inconvenicne. Thank you for your cooperation and understanding.

SRS was resumed at 18:00 on June 1. Thank you for your cooperation.

ARSA DDBJ db search temporary unavailable May. 30, 2007
ARSA is the all-round and high-speed data retrieval system provided by DDBJ through WWW. At present, DDBJ database search is unavailable due to the system error. Details are as follows:
  • Date & Time: May 30, 2007(Wed) 10:50 - (resume will be notified on this DDBj HP)
  • Suspended services: DDBJ in ARSA
  • Note: Currently, ARSA is still available except for DDBJ database search. If you would like to hasten to the search of DDBJ database, please substitute SRS.

Thank you for your understanding and cooperation.

Resumed at 23:00 on May 30. We apology for your long time inconvenience.

Program Error in Text View of WWW BLAST May. 24, 2007
In the BLAST search services via WWW, there had been errors in the results display.
Details are as follows.
  • Services:BLAST (view the result by WWW)
  • Condition:In obtaining the result by WWW, when the "Text View" is specified, alignment results were displayed up to 100 ,in spite of specifying being displayed more than 100 results.
  • Period:from February 26, 2007 10:00 to May 18, 2007 13:00
  • Cause:program error

The program error had already been fixed, and now, the correct results are available.

We apology for your inconvenicnce.

ARSA database search (DDBJ, DAD) temporary unavailable May. 15, 2007
ARSA is the all-round and high-speed data retrieval system provided by DDBJ through WWW. At the following schedule, DDBJ and DAD database search is unavailable for the database update. Details are as follows:

  • Date & Time: May 21, 2007(Mon) 9:00 - 18:00 (resume will be notified on this DDBj HP)
  • Suspended services: DDBJ and DAD search in ARSA
  • Note: During the above period, ARSA is still available except for the above 2 databases search. If you would like to hasten to the search of the above 2 databases, please substitute SRS.

Thank you for your understanding and cooperation.

SRS services unavailable by hardware accident May. 11, 2007
SRS (Sequence Retrieval System) is the keyword retrieval service provided by DDBJ WWW server. Due to the hardware accident, the service is unavailable now. If you would like to hasten to the keyword retreival, please substitute ARSA for SRS. Resume will be notified in thie page as soon as the trouble was resolved.

We apology for your inconvenicne. Thank you for your cooperation and understanding.

SRS was resumed at 14:50 on May 11. Thank you for your cooperation.

NIG Network services temporary down May. 10, 2007
NIG (National Institute of Genetics) network service will be unavailable at the following schedule because of the network maintenance.

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

Thank you very much for your understanding and cooperation.

Date & Time: May 15 (Tu) 12:00 to 14:00 (JST)
PRF Rel. 114 was released May 2, 2007
PRF (Protein Research Foundation)/SEQ database Release 114 was released on May 2, 2007 at DDBJ.
PRF Release 114 consists of 791,254 entries, and the total number of residues reached 268,739,354.

"Search & Analysis" services suspension for the maintenance Apr. 27, 2007
The following WWW and E-mail
services provided by DDBJ will be unavailable as follows;

Date & Time: May 15, 2007  9:00 - 18:00 (scheduled)
Services: FASTA, BLAST, PSI-BLAST, SSEARCH, HMMPFAM, ClustalW

Traffic, Result Viewer
Note: E-mail requests are accumulated in the mail server while services are stopping (The analysis is not executed).
After the services are resumed, the requests will be processed.
Resume will be notified in this DDBJ HP. Thank you for your understanding and cooperation.

The maintenance works was completed, and the services are resumed at 18:00.
Genome data were added to GIB Apr.27, 2007
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the following genome sequence data were released from March 20 to April 27, 2007, we incorporated them to GIB, and now you can search those data.

  • Methanococcus maripaludis C5 (by Joint Genome Institute)
  • Saccharopolyspora erythraea NRRL 2338 (by University of Cambridge)
  • Francisella tularensis subsp. tularensis WY96-3418 (by UT Southwestern Medical Center)
  • Desulfotomaculum reducens MI-1 (by Joint Genome Institute)
  • Burkholderia vietnamiensis G4 (by Joint Genome Institute)
  • Herminiimonas arsenicoxydans (by Genoscope)
  • Geobacillus thermodenitrificans NG80-2 (by Nankai University)
  • Corynebacterium glutamicum R (by RITE)
  • Aeromonas salmonicida subsp. salmonicida A449 (by NRC Institute for Marine Biosciences)
  • Prosthecochloris vibrioformis DSM 265 (by Joint Genome Institute)
  • Polynucleobacter sp. QLW-P1DMWA-1 (by Joint Genome Institute)
  • Yersinia pestis Pestoides F (by Joint Genome Institute)
  • Mycobacterium gilvum PYR-GCK (by Joint Genome Institute)
  • Pyrobaculum arsenaticum DSM 13514 (by Joint Genome Institute)
  • Rhodobacter sphaeroides ATCC 17025 (by Joint Genome Institute)
  • Salinispora tropica CNB-440 (by Joint Genome Institute)
  • Enterobacter sp. 638 (by Joint Genome Institute)
  • Pseudomonas stutzeri A1501 (by Joint Genome Institute)
  • Caldicellulosiruptor saccharolyticus DSM 8903 (by Joint Genome Institute)
  • Pseudomonas mendocina ymp (by Joint Genome Institute)
  • Shewanella putrefaciens CN-32 (by Joint Genome Institute)

Suspension of some parts of DDBJ activities during Japanese holidays Apr. 27, 2007
We at DDBJ suspend our business for releasing data and answering all inquires from April 28 to 30, and from May 3 to 6, 2007.

Search and analysis and another WWW services are available.

We will resume the normal business from May 7. Thank you very much for your understanding and cooperation.

Release of new human EST 134,569 entries Apr. 24, 2007
DDBJ newly released human EST 134,569 entries, which had been submitted by NEDO human cDNA sequencing project.
These entries were released as DDBJ daily updates on April 21.
The accession numbers are as follows;

DAD search unavailable in ARSA Apr. 24, 2007
ARSA is the data retrieval system provided by DDBJ through WWW. At present, DAD search is unavailable. Details are as follows:

DAD search is unavailable (In the "Quick Search", when the DAD is selected as the database, error message is displayed). Another functions and options can be available.


Service name: ARSA
Date: Apr. 23, 2007 4:00 - 16:20
Apr. 24, 2007 2:50 -
We apology for your inconvenicnce.

DAD search trouble was fixed. Thank you for your understanding and cooperation.(Apr. 24 16:26)

NIG Network services temporary down Apr. 19, 2007
NIG (National Institute of Genetics) network service will be unavailable
at the following schedule because of the network maintenance.

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

Thank you very much for your understanding and cooperation.

Date & Time: April 26 (Thu) 14:00 to 16:00 (JST)

The maintenance works had completed, and the network services were resumed. Thank you for your cooperation.(16:40)

Release of WGS 134429 entries and CON 6928 entries for Medaka strain Hd-rR,
and, WGS 346141 entries and CON 38235 entries for strain HNI
Apr. 18, 2007
DDBJ released WGS 134429 entries and CON 6928 entries for Medaka
(Oryzias latipes)
strain Hd-rR, and also released WGS 346141 entries and CON 38235 entries
for strain HNI. All of these data had been submitted by University of Tokyo.
These entries were released as DDBJ daily updates on April 2.

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

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

Accession numbers;

strain Hd-rR (WGS version 4)
    WGS: BAAF04000001-BAAF04134429 (134429 entries)
    scaffold/CON : scaffold/CON :DF083412-DF090103 (6692 entries)
    ultra/CON : ultra/CON :DF090104-DF090315 (212 entries)
    chromosome/CON: chromosome/CON:DG000001-DG000024 (24 entries)
strain HNI (WGS version 1)
    WGS: BAAE01000001-BAAE01346141 (346141 entries)
    scaffold/CON: DF000001-DF038235 (38235 entries)
anonymous FTP:
    Oryzias_latipes_CON_070402_1.seq.gz
    Oryzias_latipes_CON_070402_2.seq.gz
    Oryzias_latipes_CON_070402_3.seq.gz
    Oryzias_latipes_CON_HNI_070402.seq.gz
    Oryzias_latipes_WGS_070402_1.seq.gz
    Oryzias_latipes_WGS_HNI_070402_1.seq.gz

Integrated Database Renewal Apr. 18, 2007
Integrated Database of Genome Network Platform was updated on 28th March 2007.
New function of "gene comparison" is now available. About the detail, please see below.

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

Statistics [Top 30 organisms according to the total number of nucleotides] Update Apr. 17, 2007
Top 30 organisms according to the total number of nucleotides (-DDBJ rel.69)
in Breakdown statistics was updated with releasing DDBJ rel.69.
Oryzias latipes (Japanese rice fish) which entries were released as DDBJ daily updates on April 2 was ranked in 24th place.
Vitis vinifera (grape) was appeared newly in Top 30. Click the organismname to view the graph of change.

getentry suspension for the maintenance Apr. 13, 2007
getentry is the data retrieval system provided by
DDBJ through web and E-mail.

For the maintenance work, getentry will be suspended on the following day.
  • April 17, 2007 (Tuesday) 18:00 - 19:00

Note:In another DDBJ services such as ARSA, Homology Search (FASTA, BLAST, PSI-BLAST, SSEARCH) and SQmatch, viewing the result entries (invocated by getentry program) during the suspension period(You can execute the retrieval).

Thank you for your understanding and cooperation.

Maintenance works finished. Thank you for your cooperation.(19:10)

Release of new wheat EST 194,853 entriess Apr. 5, 2007
DDBJ newly released wheat EST 194,853 entries, which had been
submitted by National Institute of Genetics.
These entries were released as DDBJ daily updates on April 3.

Reference URL: 

http://dolphin.lab.nig.ac.jp

The accession numbers: CJ773323-CJ968175 (194,853 entries)

anonymous FTP: Triticum_aestivum_EST_070403_1.seq.gz

Release of new mouse EST 95,566 entries Apr. 5, 2007
DDBJ newly released mouse EST 95,566 entries, which had been
submitted by National Institute of Radiological Sciences.
These entries were released as DDBJ daily updates on April 3.

The accession numbers are as follows;

    AV442833-AV503678     AV503747-AV504941     AV504943-AV517878

    AV567729-AV568517     AV568519-AV568529     AV568531-AV568562

    AV568564-AV568588     AV568590-AV568595     AV568597-AV568605

    AV568607-AV568629     AV568631-AV570287     AV570357-AV573382

    AV573409-AV576847     AV576917-AV577109     AV577169-AV588547

anonymous FTP:
Mus_musculus_EST_070403_1.seq.gz

DDBJ Rel. 69 Completed Apr. 2, 2007
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public. We completed DDBJ Release 69 in March. 30, 2007.
DDBJ Release 69 consists of 67,523,680 entries, and the number of bases reached 71,775,679,500.

FTP site for periodical release and new data download

Temporary suspension of GIB Mar. 27, 2007
GIB service is unavailable now.

Resume will be notified in this DDBJ HP. Thank you very much for your understanding and cooperation.

GIB was resumed at 11:10 on March 27. Sorry for your inconvenience.

Emergency Suspension of "Search & Analysis" services Mar. 23, 2007
The following WWW and E-mail services provided by DDBJ will be unavailable for 2 hours today.

Date & Time: March 23, 2007 15:00 - 17:00(scheduled)
Services: ARSA
ClustalW
getentry
Homology Search (FASTA, BLAST, HMMPFAM, PSI-BLAST, SSEARCH)
Resume will be notified in this DDBJ HP.
Although this is an urgent notice, DDBJ will appreciate your understanding and cooperation.

Maintenance works finished. Thank you for your cooperation.(17:00)

Temporary suspension of "homology search" and "ClustalW" by E-mail Mar. 23, 2007
DDBJ provide homology search services and ClustalW via WWW and by E-mail.
Among these services, E-mail use methods are temporary suspended. Details are as follows.

*Services: BLAST, FASTA, HMMPFAM, PSI-BLAST, SSEARCH
ClustalW
*Period: From March 23, 2007 19:00
*Cconditions: Among the services, when the following methods are selected, the results are not returned (sending the query is acceptable).
   send by WWW --> receive by E-mail
   send by E-mail --> receive by E-mail
*Use of service: Please select "send by WWW --> receive by WWW" method. At present, this methods works normally.
*Resume: Resume will be notified on this DDBJ HP.

We apology for your inconvenicnce.

Link Error in the homology search results display Mar. 23, 2007
In the homology search services which DDBJ provide via WWW and by E-mail, we found there had been link errors in the results display. Details are as follows.

*Services: BLAST, FASTA, PSI-BLAST, SSEARCH
*Period: February 27, 2007 - March 17, 2007 11:00
*Cconditions:

  • In the result view screen¡¤because LOCUS name had been mislocated in the position of accession numbers,(see below)
  • When you check your results in Result Viewer, if you did the search during the above peiord, there are the same error.
*Result The search Result is correct.
---------------------------------------------------------------------
                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AAU58946|U58946.1 Aspergillus awamori transposable element Tan1,...   3979  0.0  
    (Above is the Locus name, and "link" did not work correctly)
AM270150|AM270150.1 Aspergillus niger contig An07c0330, complete...   3866  0.0  
AM270394|AM270394.1 Aspergillus niger contig An18c0010, complete...    517  e-143
AM270353|AM270353.1 Aspergillus niger contig An16c0010, complete...    517  e-143
---------------------------------------------------------------------
*Measure The databases for homology searches was reconstructed. (Reconstruction works had already been completed on March 17.)
Now the service works normally. We apologize for your inconvenience.

PRF Rel. 113 was released Mar. 20, 2007
PRF (Protein Research Foundation)/SEQ database Release 113 was released on Mar. 19, 2007 at DDBJ. PRF Release 113 consists of 773,622 entries, and the total number of residues reached 262,963,464.
Genome data were added to GIB Mar 20, 2007
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the following genome sequence data were released from February 20 to March 20, 2007, we incorporated them to GIB, and now you can search those data.

  • Streptococcus sanguinis SK36 (by Virginia Commonwealth University)
  • Clostridium thermocellum ATCC 27405 (by Joint Genome Institute)
  • Methanoculleus marisnigri JR1 (by Joint Genome Institute)
  • Shewanella baltica OS155 (by Joint Genome Institute)
  • Actinobacillus pleuropneumoniae L20 (by Joint Genome Institute)
  • Staphylothermus marinus F1 (by Joint Genome Institute)
  • Mycobacterium sp. JLS (by Joint Genome Institute)
  • Pyrobaculum calidifontis JCM 11548 (by Joint Genome Institute)
  • Burkholderia mallei NCTC 10247 (by The Institute for Genomic Research)
  • Burkholderia pseudomallei 1106a (by The Institute for Genomic Research)
  • Burkholderia pseudomallei 668 (by The Institute for Genomic Research)
  • Rhodobacter sphaeroides ATCC 17029 (by The Institute for Genomic Research)
  • Acinetobacter baumannii ATCC 17978 (by Yale University)
  • Prochlorococcus marinus MIT 9301 (by J Craig Venter Institute)
  • Shewanella loihica PV-4 (by Joint Genome Institute)

Release of new tammar wallaby (Macropus eugenii) GSS 147,312 entries Mar.14, 2007
DDBJ newly released tammar wallaby (Macropus eugenii) GSS 147,312 entries,
which had been submitted by RIKEN Genomic Sciences Center.
These entries were released as DDBJ daily updates on Mar. 10.

getentry is resumed and the search options are available Mar.13, 2007
getentry is the data retrieval system provided by DDBJ through web and E-mail.

The following search options that interrupted in
"Apology for the getentry access trouble (on February 28)" was restored.
We apologize for troubling you.

search options: Locus Name
&nbsp Gene Name
&nbsp Product Name
&nbsp Clone Name
Thank you for your understanding and cooperation.

Apology for access trouble to getentry Mar. 13, 2007
getentry is the data retrieval system provided by DDBJ through web and E-mail.

From 14:00 to 15:30 on March 12, there was a trouble for accessing to getentry. Now getentry is available. Sorry for your inconvenience.

Thank you for your understanding and cooperation.

getentry suspension for the maintenance Mar. 12, 2007
getentry is the data retrieval system provided by DDBJ through web and E-mail.

Since February 27, some search options have been unavailable because of the trouble which happened on that day.
To recover these options, getentry will be suspended today at the following time.
  • March 12, 2007 (Today) 18:00 - 19:00

Thank you for your understanding and cooperation.

Cancellation of the requests in DDBJ's "Search & Analysis" services due to System change in NIGMar.9, 2007
According to the NIG computer system replacement conducted in this February, DDBJ switched the "Search & Analysis" service system to the present new system.
After switching, the old search system terminated receiving the requests, and stopped its operation as of March 9, 2007 at 17:00.

Because the requests which had been received by the old system (FASTA, BLAST, PSI-BLAST, SSEARCH, ClustalW) could not be transferred to the current system, all the requests which had not been completed their execution by the termination of the old system was cancelled.

If you sent your request to DDBJ's Search & Analysis system before Feb. 27, and if you have not received the result yet, please send your request again (Now, all the request are received by the new system).

Thank you for your understandint and cooperation.

"Search & Analysis" services emergency suspensionMar. 9, 2007
The following WWW and E-mail services provided by DDBJ will be unavailable for 1 hour today.

Date & Time: March 9, 2007 16:00 - 17:00(scheduled)
Services: ARSA

ClustalW
getentry
Homology Search (FASTA, BLAST, PSI-BLAST, SSEARCH, HMMPFAM)
Resume will be notified in this DDBJ HP.

Although this is an urgent notice, DDBJ will appreciate your understanding and cooperation.

Maintenance works finished. Thank you for your cooperation.(17:30)

Apology for not updated of Anonymous FTP - TPA and CON - (INSD-XML) in
DDBJ Rel. 68
Mar. 9, 2007

NIG and DDBJ services emergency suspension Mar. 5, 2007
Because of the trouble of electric power supply facilities, all NIG and DDBJ services was unexpectedly suspended at midnight of March 3. Details are as follows.
  • Period: March 3, 23:20
  • Status*all NIG and DDBJ services was unexpectedly suspended
  • Resume:as of March 5, 11:00 All services were resumed.

Thank you for your cooperation and understanding
URL change of getentry Mar. 2, 2007
getentry is the data retrieval system provided by DDBJ through web and E-mail.

The computer system in the National Institute of Genetics has replaced in this March. According to this replacement, URL of getentry has changed to http://getentry.ddbj.nig.ac.jp/top-e.html. Please update your links to this new URL.
Thank you for your understanding and cooperation.
Apology for access trouble to getentry Feb. 28, 2007
getentry is the data retrieval system provided by DDBJ through web and E-mail.

In the night of February 27, there was a trouble for accessing to getentry. The details are as follows:

Access downtime: February 27, 2007 21:03 - 22:15
Current Status: Currently, getentry is available other than the following search options.
  • Locus Name
  • Gene Name
  • Product Name
  • Clone Name
Resume will be notified at this DDBJ HP. Thank you for your understanding and cooperation.

All services were resumed. (Mar. 13)
Full-length cDNA sequening of brain-expressed gene of cynomolgus monkey in PLOS Biology Feb. 19, 2007
Full-length cDNA sequening of brain-expressed gene of a cynomolgus monkey, Macaca fasciculariswas reported in PLOS Biology, and appeared in January as an online version.

In this paper, full-length cDNA sequencing on the brain transcriptome of an Old World monkey (OWM) was carried out, and then conducted comparative analysis among human, OWM, chimpanzee, and mouse. Authors belongs to the reserach institute and/or university in Japan, Taiwan, and USA. Dr. Takashi Gojobori, director of Center for Information Biology and DNA Data Bank of Japan(CIB-DDBJ), is one of the authors.

Brains of higher primates have evolved rapidly, whereas brain-expressed genes are known to evolve slowly in mammals. In human, there are a lot of questions between the rate of evolution of brain-expressed genes and evolution of the brain itself. To clear this questions, comparative study of the variation of the DNA sequences of various species is necessary.

The data was submitted to DDBJ/EMBL/GenBank International Nucleotide Sequence Databases and was released under the Accession numbers AB170063 - AB174733. The sequence information is available via DDBJ anonymous FTP (whole data download) or getentry system.

Genome data were added to GIB Feb. 19, 2007
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.

Because the following genome sequence data were released from January 26 to February 19, 2007, we incorporated them to GIB, and now you can search those data.

  • Methylibium petroleiphilum PM1 (by Joint Genome Institute)
  • Lactococcus lactis subsp. cremoris MG1363 (by Bielefeld University)
  • Methanocorpusculum labreanum Z (by Joint Genome Institute)
  • Burkholderia mallei NCTC 10229 (by The Institute for Genomic Research)
  • Streptococcus pyogenes Manfredo (by Sanger Institute)

Update of "Conference on Information Biology" Feb. 15, 2007
Following conferences were added to "Conference on Information Biology"

Termination of SSThread service Feb. 2, 2007
DDBJ will terminate providing SSThread service (Prediction of protein secondary structure using threading) at WWW and Email, as of Feb. 23. Thank you for using this service for a long time.

Important: Temporary halt of the DDBJ activities in February, 2007 Jan. 29, 2007
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 the following schedule.

SAKURA suspension:

  • From February 22 (Tue) 17:00 to February 28 (Wed) 9:00
If you plan to submit your data to DDBJ and obtain accession numbers in February, 2007, please keep the period mentioned above in mind. Thank you very much for your understanding and cooperationin advance.

ARSA suspended for the urgent maintenance Jan. 29, 2007
Because of the emergency maintenance, ARSA service is unavailable now. Thank you very much for your understanding and cooperation.

ARSA was resumed at 17:00 on January 29. Sorry for your inconvenience.
Genome data were added to GIB Jan. 25, 2007
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 27 (2006) to January 25 (2007), we incorporated them to GIB, and now you can search those data.

  • Prochlorococcus marinus AS9601 (by J Craig Venter Institute)
  • Prochlorococcus marinus MIT 9515 (by J Craig Venter Institute)
  • Prochlorococcus marinus NATL1A (by J Craig Venter Institute)
  • Prochlorococcus marinus MIT 9303 (by J Craig Venter Institute)
  • Hyperthermus butylicus DSM 5456 (by University of Copenhagen)

Mirroring H-Invitational DB suspension for system maintenance Jan. 22, 2007
Mirrorring H-Invitational DB will be unavailable for a while because of the system maintenance. Resume will be notified on this DDBJ HP. H-Invitational Database CIB-DDBJ Flat File server (full-length cDNA sequence database) is still available.

Thank you very much for your understanding and cooperation.
ClustalW DOTSINOUTPUT option is available Jan. 22, 2007
DDBJ provides ClustalW services through WWW and E-mail. The DOTSINOUTPUT option(The mached characters of the alignment are displayed by the dots) is available for ALIGNMENT, but unavailable together with the "TREE" and/or "BOOTSTRAP" options. DOTSINOUTPUT option is the DDBJ's original options in the ClustalW.
Termination of CAMUS Database service Jan. 19, 2007
DDBJ will terminate providing CAMUS database service (compressed database for homology seraches) at WWW, as of Feb. 23. Thank you for using this database for a long time.
DAD rel. 38 was released Jan. 19, 2007
DDBJ amino acid database (DAD) Release38 was released on Jan. 19, 2007 at DDBJ. DAD Release 38 consists of 3,721,922 entries, and the total number of residues reached 1,138,376,646.

FTP site for DB download
Update of "Conference on Information Biology" Jan. 16, 2007
Following conferences were added to "Conference on Information Biology"

Statistics [Top 30 organisms according to the total number of nucleotides] Update Jan. 15, 2007
Top 30 organisms according to the total number of nucleotides (-DDBJ rel.68)
in Breakdown statistics was updated with releasing DDBJ rel.68.
Ascaris suum (large roundworm of pigs) was ranked in Top 30. Click the organismname to view the graph of change.

NIG Network services temporary down Jan. 12, 2007
NIG (National Institute of Genetics) network service will be unavailable at the following date, because of the preliminary works for the computer system replacement in NIG scheduled in this March. All DDBJ network services and NIG supercomputer (supernig and minerva2) service will also be unavailable.

Date & Time:

  • From January 26 (Fri) 17:00 to January 28 (Sun) 13:00

  • From February 3 (Sat) 9:00 to February 4 (Sun) 18:00
According to this suspension, SAKURA will also be unavailable for the following schedule.

SAKURA suspension:

  • From January 26 (Fri) 15:00 to January 29 (Mon) 9:00

  • From February 2 (Fri) 15:00 to February 5 (Mon) 9:00
Thank you very much for your understanding and cooperationin advance.
Report for DDBJ activicies in NAR Jan. 11, 2007
The new and significant DDBJ activities of the past year were introduced in the following paper appeared in Nucleic Acids Research Vol.35 Database Issue (Jan. 1).
"DDBJ working on evaluation and classification of bacterial genes in INSDC"
Hideaki Sugawara, Takashi Abe, Takashi Gojobori and Yoshio Tateno
Nucleic Acids Research, 2007, Vol. 35, Database issue D13-D15
(Summary) DDBJ newly collected and released nucleotide sequence data containing honeybee expressed sequence tags (ESTs), re-examined and re-annotated complete genome data of Escherichia coli K-12 W3110, medaka WGS and human MGA, in the period from July 2005 to June 2006. DDBJ also systematically evaluated and classified the genes in the complete bacterial genomes submitted to INSDC. (PMID: 17108353)

NIG network service temporary down due to electric power interruption Jan. 9, 2007
NIG network service affectd by the electric power interruption which had occured on Jan. 9. Details are as follows:

    Period: Jan. 9 (Tue) 09:40 - 10:30

    Affectd service: NIG network service

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

ARSA was resumed at 9:00 on January 10. Sorry for your inconvenience.
DDBJ Rel. 68 Completed Dec. 28, 2006
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public. We completed DDBJ Release 68 in Dec. 28, 2006. DDBJ Release 68 consists of 64,267,978 entries, and the number of bases reached 68,259,314,742. We changed the maximum file size from 300 MB to 1.5 GB

FTP site for periodical release and new data download
Update of "Conference on Information Biology" Dec.28, 2006
Following conferences were added to "Conference on Information Biology"

  • Plant and Animal
    Genome XV Conference (1/13-17)
  • target="_blank">EMBO Workshop: Viral RNA: Structure, Function and
    Targeting (3/5-7)

  • Computational Cell Biology (3/6-9)
  • Systems Biology and Regulatory Networks (3/21-27)
  • Systems Biology:Global Regulation of Gene Expression
    (3/29-4/1)
  • BSDB 2007 Spring Symposium (3/29-4/1)
  • Experimental
    Biology 2007
    (4/28-5/2)
  • From basic
    genomics to systems biology
    (5/2-4)
  • EMBO Conference on Chromatin and Epigenetics
    (5/3-6)
  • HGM2007 in Montreal (5/21-24)
  • GENSIPS
    2007
    (6/10-12)
  • EVOLUTION
    2007 (6/16-20)
  • Regulation of protein function by SUMO modification
    (6/25-27)
  • DILS
    2007 (6/27-29)
  • CIBB 2007 -
    Fourth International Meeting on Computational Intelligence Methods for
    Bioinformatics and Biostatistics )
    (7/7-10)
  • EURO-CBBM Workshop (7/8)
  • 18th
    Annual Symposium on Combinational Pattern Matching (7/9-11)
  • 6th
    European Biophysics Congress
    (7/15-19)
  • 7th Atlantic Symposium on Computational Biology & Genome
    Informatics (7/15-22)
  • The 2007 annual meeting of the Society for Industrial
    Microbiology (7/29-8/2)
  • ELSO 2007 (9/1-4)
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