Last updated:2015.12.24.

What’s New(2008)

(Urgent)ARSA is unavailable Jan.5, 2009
ARSA is a high-speed data retrieval system provided by DDBJ via WWW and Web API .
Because of the system trouble broken out during the holidays, at present, ARSA is unavailable.
We will announce on this page when they resume.
Thank you for your cooperation.
The service was resumed (at 11:00).
Suspension of the DDBJ activity during the New Year Holidays Nov. 28, 2008
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 5th(Mon), 2009.
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 27th(Sat), 2008 to January 4th(Sun), 2009
       SAKURA suspension: from December 25(Thu), 2008 at 17:00(JST) to January 5th(Mon), 2009 at 10:00(JST)
       data release suspension: from December 25th(Thu), 2008 to January 5th(Mon), 2009

Thank you very much for your understanding and cooperation.
We wish you a Happy New Year.

DDBJ Rel. 76 Completed Dec.24, 2008

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

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

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

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

The accession numbers are as follows;

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

Related site:

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

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

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

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

    ARSA

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

 

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

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

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

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

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

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

DDBJ services suspension schedule:

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

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

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

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

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

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

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

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

The accession numbers are as follows;

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

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

Related site:
  • NIG DNA Sequencing Center

  • PHYSCObase

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

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

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

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

We sincerely apologize for your inconvenience.

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

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

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

    Date: Aug. 21 (Thu) 18:15

    Affectd service: NIG network service

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

    Following services are still unavailable:

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

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

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

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

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

These data are now available.
Termination of a part of DDBJ servicesAug 15, 2008
DDBJ discontinues the following services provided by WWW and by E-mail, as of the described schedule. We apologize for your inconvenience. Thank you for your understanding and cooperation.

Services substitute services of DDBJ
Search & Analysis by E-mail server
  getentry 2008.9.12 (terminated) getentry (WWW*1WAB*2
  get-version 2008.9.12(terminated) getentry (WWW*1WABI*2
  FASTA 2008.9.12(terminated) FASTA (WWW*1WABI*2
  BLAST 2008.9.12(terminated) BLAST (WWW*1WABI*2
  SSEARCH 2008.9.12(terminated) SSEARCH (WWW*1
  ClustalW 2008.9.12(terminated) ClustalW (WWW*1WABI*2
  HMMPFAM 2008.9.12(terminated) HMMPFAM (WWW*1
Keyword Search
  SRS 2008.12.26(terminated) ARSA ==>Termination of SRS
Sequence Pattern Match
  SQmatch 2008.11.14(terminated)  
Protein Compatibility Analysis, etc.
  PDB Retriever 2008.11.14(terminated)  
  Libra 2008.11.14(terminated) GTOP
  Lib score 2008.11.14(terminated)  

*1:Receiving the results by E-mail after sending the queries by WWW is continuously available.
*2:WABI stands for Web API for Biology and can be called by programs written by Perl, Java, C, Ruby and Python (ref: http://www.xml.nig.ac.jp/)

DDBJ terminated SRS (Sequence Retrieval System) service as of
December 26, 2008. Please use ARSA hereafter.

Termination of providing SRS(Sequence Retrieval System) services

DDBJ terminates providing SRS services (by WWW and WABI ) as of the December 26, 2008. We appreciate very much that you have used SRS since it was firstly launched in DDBJ in 1999. We apologize for your labor switching your keyword search system from SRS to ARSA, but, we hope ARSA is useful for all DDBJ users. Please refer the summary of ARSA and SRS shown in below.



(1)ARSA and SRS Search functions

A R S A S R S
Search
Engine
High-speed XML database search engine "Interstage Shunsaku" was applied for the nucleotide sequence database retrieval Keyword search system developed by EBI(European Bioinformatics Institute) was applied and reconstructed for the DDBJ database retrieval
Key
Features
  • Rapid response: Even in any complex search keys, the results are returned within 5 seconds
  • In the DDBJ database retrieval, any combination of feature/qualifiers used in the DDBJ flat file format can be specified as search keys
  • Wide variety of WEB API programs such as SOAP/REST is applicable
  • From Quick Search (simple keyword search) to Advanced Search (specify a complex search queries), multistage search condition can be selectable.
  • Wide variety of WEB API programs such as SOAP/REST is applicable


functions ARSA SRS
Cross search of multiple DB Yes Yes
Specifying the search field Yes Yes
Use of DDBJ flat file Feature/Qualifier Yes No
Quick search Yes Yes
Multiple keywords connection using and/or/not Yes Yes
Relation to analysis tools Yes Yes
Speed fast slow

:Use of "not" in Quick Search is in being enhanced (as of Aug. 2008)


(2)ARSA Improvement History

    No. of
DBs
2004.12 Trial operation started at the DDBJ HP
"DDBJ" and "DDBJNEW" only
 2 
2005.12 Upgraded
Full-time operation started
 
2007.02 21DBs other than DDBJ was added  23 
2007.07 Extensive Enhancement and transfer to Official Operation
<Main New Functions>

  • The search results can be downloaded across databases
  • Change of the displayed items in the result view screen is possible
  • API(Application Program Interface) for Java/Perl was enhanced
 
2007.10 DDBJ HP design renewal
(ARSA is available at the search window of DDBJ HP)
 
2007.10 Sequence search program linked to TX Search was changed from SRS to ARSA  
2007.11 Further Upgrade subsequent to enhancement conductted in July"
<Main new functions>

  • Addition of KEGG Pathway Database
  • Specification of detailed search conditions in the all databases, as well as DDBJ
  • Cross search by the common search queries
 24 
2008.05 Removal of redundant DBs
4DBs related to PFAM were removed
 20 



(3)Usage of ARSA and SRS

In the Page View count, ARSA exceeded SRS in March, 2008.



Unique User:a number of an individual that has visited a Web site or received specific content,for a specified period of time such as a day or month. More than one time visits by the same user is counted as 1.
Page View:a request to load a single page of an Internet site. This number is widely used as an access index to the site


(4) Conclusion
DDBJ, since starting the ARSA services in December of 2004 as a trial operation, has built up continuous improvements for the more convenient keyword search system. Meanwhile, DDBJ has introduced ARSA at the scientific meeting and DDBJing tutorials. The increase of ARSA users reflects these efforts, and as a result, DDBJ decided to terminate providing SRS service.
DDBJ will do all the more efforts for the development of ARSA. If you have any comments for ARSA, please send it from "Your Comment" which is located in the upper blue zone.

DDBJ starts accepting Trace Archive data constructing it as a part of the integrated database project. Aug 6, 2008
Trace Archiveis defined by NCBI as a permanent repository of DNA sequence chromatograms (traces), base calls, and quality estimates for single-pass reads from various large-scale sequencing projects.





DDBJ has reached the first registration of Trace Archive data in July 2008, supported by National project of integrating life science databases.

1. Trace data of Oryzias latipes WGS sequences determined by National Institute of Genetics (NIG):
TI numbers are as follows:

  • 2095022956-2095389675
  • 2095396176-2096435759
  • 2096858496-2096933759

* Relevant announcement: Release of WGS 134,429 entries and CON 6,928 entries for Medaka strain Hd-rR, and WGS 346,141 entries and CON 38,235 entries for strain HNI.

2. Trace data from human gut metagenome project by University of Tokyo, the Center for Omics and Bioinformatics (UTCOB):
TI numbers are as follows:

  • 2097946941-2099007079



*Relevant announcement:Release of new human gut metagenome WGS data, 353,805 entries.

(1) Assemble trace data to WGS entries.
The sizes of these trace data are as follows:
(a) about 50G bytes(from NIG, gzipped tar files including .qual, peak, .seq and .scf)
(b) about 40G bytes(from UTCOB, gzipped tar files including .scf)
These trace data both (a) and (b) were assembled to WGS entries:
The (a) trace data was firstly assembled to the part of BAAF WGS entries (about 309M bytes, gzipped tar file including Flat File format). The trace data (a) was further assembled to DG000001-DG000024 chromosome /CON entries. Medaka genome sequencing project web site provides more details.
The trace data (b) was assembled to BAAU-BABG WGS entries (about 272M bytes, gzipped tar file including Flat File format).
(2) Transfer the file from DDBJ to NCBI .
We uploaded test data to NCBI Trace Archive by the conventional ftp protocol. It took intolerably long time to transfer. We have investigated several alternative file transfer protocol and application. Then, we have been able to transfer by parallel transfer of multiple files by the conventional ftp. The transfer was actually completed in several hours though it was expected 2 whole days based on a sequential ftp.

These data are now retrievable at NCBI Trace Archive. DDBJ starts preparing the original web page for the retrieval of trace data.

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

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

Thank you very much for your understanding and cooperation.

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

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

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

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

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

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


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

We sincerely apologize for your inconvenience.

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

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

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

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


  • Condition :

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

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

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

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

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

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

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

We sincerely apologize for your inconveniece.

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

The accession numbers are as follows;

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

FTP site for DB download : Drosophila_EST_080614_1.seq.gz
[Monthly DDBJ Topic(June, 2008)] The number of nucleotides released from INSD has reached 200 G bases Jun 6, 2008
In May 2008, the total number of bases ( DNA and RNA ) collected and distributed by INSD ( International Nucleotide Sequence Database: DDBJ/EMBL/GenBank ) has reached 200 G bases (200,000,000,000 bases; the 'letters' of the genetic code). It took only three years from when we had reached 100G bases on August 2005.


INSD has expanded its specifications to accept data submissions from large scale sequencing projects. For example, we have started accepting the sequence data from EST (Expressed Sequence Tags) projects into EST division since 1993. On 2002, to accept submissions of the draft genome and the meta-genome sequences, we have created the new category for WGS (Whole Genome Shotgun) data.


The left figure shows the relationship of the ratios of three categories. The right figure shows the numbers of bases.

As you can see in the right figure, base counts of both WGS and EST/GSS (Genome Survey Sequences) data increased approximately two times during three years. The base count of WGS data has increased 100 G bases only past 6 years.



What is WGS data?
In general the term, WGS "Whole Genome Shotgun", originally means an approach to sequence genomic DNA molecules that are once fragmented into millions of pieces, which are sequenced and reassembled to produce a series of sequences,. The strategy was firstly adopted to sequence the complete genome of Haemophilus influenzae in 1995. In INSD, the large set of contigs or the finished sequences without annotation from the proceeding genome project can be accepted as WGS data.


Future improvement
Increasingly High-Throughput Sequencing (HTS) technology (also called the next generation sequencers) is gaining popularity. It will accelerate the increase ratio of sequence data submitted to DDBJ. For the vast quantities of future submissions, DDBJ has to improve our database systems.


NCBI has started making SRA (Short Read Archive) to collect the raw outputs of short piece data derived from the next-generation sequencer, such as 454, Solexa, SOLiD and so on. As well as EBI, DDBJ is planning to collaborate with SRA.
Related to the new sequencing technologies, INSD faces many requests for the deposition of assembled EST (or EST-like short piece of) sequences. Therefore we will prepare a new division, TSA (Transcriptome Shotgun Assembly), to accept assembled sequences derived from transcriptome projects.


The day of reaching to 300 G bases
In February 2008, NIH announced about the 1000 Genomes Project, and they already sequenced human genome data between 200 to 300 G bases in their count. Related to this kind of project, it is not enough for DDBJ to accept huge scale of nucleotide sequences.


Because research communities require not only the text based nucleotide sequences, but also the raw outputs of trace data for the sequences to investigate reliabilities of sequence data, evaluation of polymorphisms among individuals and so on. Trace Archive has accepted huge number of trace data registration, more than tens of terabytes (1013 order) in their total size. Last year, DDBJ started to accept a part of trace data from Japanese researchers for the first trial. It is supported by the Integrated Database Project.


Research analyses of large scale sequences will intend to the peta byte (1015 order) data. Considering with only the size of sequence data in INSD (i.e. excluding SRA and Trace Archive), the number of nucleotides is possible to be 400 G bases or more in one and a half year later.

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

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

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

We sincerely apologize for your inconveniece.

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

 

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

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

The accession numbers are as follows;

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

FTP site for DB download :

Genome Standards Consortium created a new genome description guideline May. 22, 2008
The Genomic Standards Consortium (GSC) has created a new guideline entitled "MIGS", for the description of genomes (and metagenomes) information, and published it in "Nature Biotechnology" appeared in the issue of May 9. According to the issue of the paper, the GSC announced the press release.

Press release - 9 May 2008
Issued by the Centre for Ecology & Hydrology, UK
Nature Biotechnology 26, 541 - 547 (2008)
about GSC
MIGS

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

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

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

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

PFAMA and PFAMB are continuously available.

Thank you very much for your understanding and cooperation.

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

DDBJ mail magazine No. 37 was released May. 15, 2008
DDBJ mail magazine No. 37 was released. This site covers information about novel
services and latest news.
DDBJ is one of the three members of INSDC: "International Nucleotide Sequence Databases Collaboration", collaborating with EMBL-Bank at EBI in Europe and GenBank at NCBI in USA. The three databanks collaborated to construct the Internatilnal Nucleotide Sequence Database for more than 20 years.


To operate and implement the collaborative construction of the International Nucleotide Sequence Database, the three databanks hold the International Collaborators Meeting (ICM) every year, since the 1st ICM in Heidelberg, Germany in July, 1988. ICM is held annually rotating the host bank among the three, and the 21st one will be held at the National Institute of Genetics from May20 to 22, 2008.


Thanks to modern digital technologies, quite a few video conferences are organized for international communication and discussion, namely, attendees join the virtual meeting at their office or even at home. But, at an ICM meeting, members of the three banks meet "face-to-face", and discuss various issues at the same place for three whole days. This is one of the secrets why INSDC has been successful for 2 decades.


The ICM have always spotlighted the topics which reflect the progress of research and development in biology. Consequently, many important topics were decided at the past meetings.
They include the abolishment of the length limitation of a submitted sequence, Whole Genome Shotgum(WGS) and Third Party Annotation(TPA) data submissions, establishment of new divisions of sequences such as CON, GSS and ENV, and others. The non-protein coding sequence is one of the recent issues.
Following the decision at an ICM the common annotation manual among the three banks, Feature Table Definition Document (FT-Doc) is updated every year.


The preparation of the agenda items of the 21st ICM is in progress now. Almost 10 days from now, intensive discussion will begin at NIG, Mishima.

References:
icm2000 icm2006 icm2000

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

The accession numbers are as follows;

DK000001-DK265853 (265,853 entries)

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

FTP site for DB download : Oryzias_latipes_EST_080502_1.seq.gz

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

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

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

We sincerely apologize for your inconvenience.

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

The accession numbers and numbers of entreis are as follows;

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

FTP site for DB download

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

Thank you very much for your understanding and cooperation.

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

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

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

FTP site for DB download

 

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

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

We apology for your inconvenicne.
[Monthly DDBJ Topic(April, 2008)] Have you ever seen DDBJ? Apr. 4, 2008
Drs Hideaki Sugawara (Director of Center for Information Biology and DNA Data Bank of Japan (CIB-DDBJ), NIG) and Yoshio Tateno (Director of DNA Data Bank of Japan, NIG) had retired from the National Institute of Genetics on March 31st but appointed to be the staff of DDBJ for one year on April 1st. Professor Hideaki Sugawara provides some slides from his final lecture in the institute on March 21st to introduce you "behind the curtain" of DDBJ.
Dr. Hideaki Sugawara received the WFCC award Apr. 1, 2008
Dr. Hideaki Sugawara, Professor of National Institute of Genetics and Director of Center for Information Biology and DNA Data Bank of Japan (CIB-DDBJ) was elected as one of the Honorary Membership of the World Federation for Culture Collections (WFCC) on March 16, 2008, and was presented the inaugural WFCC Medal Award for his long time outstanding contribution to the WFCC activities.


Dr. Sugawara, has been committing to the worldwide activities of the WFCC over many years in particular to Newsletter editing, training, information dissemination, providing statistics on collections worldwide and not least the direction of the World Data Centre for Microorganisms(WDCM). He constructs and maintains the WDCM web site on his own laboratory web site. Through this web site, he continued to provide the scientific community for the microorganism researchers, as well as spread the useful information to all over the world. More recently he also contributed to establishment of OECD Global Biodiversity Information Facility (GBIF)) and the design of OECD Global Biological Resource Centre Network.


Appreciating his contribution to the WFCC for these years, the WFCC decided to elect him to the Honorary Membership of the WFCC and present the WFCC Medal, on the occasion of his retirement from the National Institute of Genetics(NIG). For the presentation ceremony, Dr. Ken-Ichiro Suzuki, Vice-President of the WFCC (and director of National Institute of Technology and Evaluation(NITE)) visited Mishima-city (where NIG is located) on March 24, 2008. Dr. Suzuki read for the message of Dr. David Smith, President of the WFCC, and handed the award medal to Dr. Sugawara. Many DDBJ staffs congratulated his honor at the ceremony, together with his family.

Dr. Suzuki presented the certificate certificate WFCC medal (small red box)

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

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

 

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

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

The accession numbers are as follows;

DH508174-DH839445 (331,272 entries)

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

Anonymous FTP:Rattus_norvegicus_GSS_080325_1.seq.gz

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

The accession numbers are as follows;

ADAAA0000001-ADAAA0005988 (5,988 Entries)

ADAAB0000001-ADAAB0006146 (6,146 Entries)

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

Anonymous FTP: AD_resource_index

Related URL: about MGA entry

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

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

Thank you very much for your understanding and cooperation.

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

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

Details are as follows:

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

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

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

    DDBJNEWr73.014.CON.gz: Including the fixed enties.
  • Cause: A software problem in the flatfile making process.
  • Current status: We have already fixed and deleted the invalid version entries
    in 2008/03/08 on the getentry and annonymous FTP (Daily update).
We apologize for our mistake very much.
[Monthly DDBJ Topic(March, 2008)] The directory of anonymous FTP was changed Mar. 7, 2008
We DDBJ changed the anonymous FTP structure.The key changes lists are following,

Changed directory names and structure
There were divided into ddbj_database (the DDBJ data) and mirror_database (the other databases data) directories though the DDBJ data and the other databases data were put together in the database under a top directory so far.

---PAST---
ftp://ftp.ddbj.nig.ac.jp/database/ :from the DDBJ data and from the other databases
---NOW---
ftp://ftp.ddbj.nig.ac.jp/ddbj_database/ :from the DDBJ data
ftp://ftp.ddbj.nig.ac.jp/mirror_database/ :from the other databases data

Kind README
Detailed data in the ddbj_database¡¤we made README.TXT
- Notice -
The Old directory(database) will be maintained one month. When regularaly watch, please change to the new directories.
Pict1. A top position of anonymous FTP(2008.2.26)

Pict2. A part of README.TXT
[Monthly DDBJ Topic(March, 2008)] DDBJ started to release patent DNA by KIPOMar. 7, 2008
We DDBJ released the patent data as a nucleotide sequence and an amino acid sequence that was accepted by Korean Intellectual Property Office (KIPO) and that being able to distribute. The KIPO's patent data is first time distribution. We released that data at February 21, 2008.


Number of nucleotide sequence: 168,562 entries (93,982,299 base-pair)
Number of amino acid sequence: 113,555 entries (16,499,605 amino-acid)


---Note---
Besides the data of KIPO, International Nucleotide Sequence Database (INSD) (collaboration of DDBJ, EMBL and GenBank) distribute other patent data that was accepted by Japan Patent Office (JPO), European Patent Office (EPO) and United States Patent and Trademark Office (USPTO).
For details, please refer to "Nucleotide Sequences Included Patent Applications" section of Patent, Intellectual Property and Priority page.

The prefix of the accession number of KIPO patent is "DI". Please refer from the following to the example of the open to the public data.

(ex) DI000001

---Note---
So, the prefixes for patent related data are;
JPO: E, BD, DD, DJ
EPO: A, AX, CQ, CS, FB
USPTO: I, AR, DZ, EA
KIPO: DI

The following figure shows summary of TOP 10 of number of ORGANISM in KIPO entries.

This announce introduced the applied data from KIPO that distributed first time. In the future, DDBJ and KIPO will build a mechanism that regular acquisition and distribution KIPO data.

韓国特許出願の塩基配列データが DDBJ より公開 2008.3.3
DDBJ/EMBL/GenBank 国際塩基配列データベース(現在,DDBJ,EMBL,GenBankの三大データバンクはINSDC(International Nucleotide Sequence Database Collaboration)と呼ばれています。)」には,日本特許庁 (JPO),からの特許データの他に, 欧州特許庁 (EPO),米国特許 商標庁 (USPTO) が受理し公開可能となった特許データも,それぞれ EMBL, GenBank を経由し,公開されています。また,2008年2月より韓国特許庁 (KIPO) からも特許出願に含まれる塩基配列データが,DDBJ に取り込まれ,公開する仕組みが確立されました。
この度公開された,韓国特許庁 (KIPO) からの特許出願塩基配列データは以下の通りです。

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

どちらも getentry より検索可能です。

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

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

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

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

These entries are searchable by getentry.

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

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

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

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

GIB is unavailable for the urgent maintenance Feb. 26, 2008
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because of the urgent maintenance works, GIB is unavailable now. Resusme will be notified on this DDBJ HP. Thank you for your cooperation.
The service was resumed at 16:22 on Feb. 26. Thank you for you cooperation.
[Monthly DDBJ Topic(Feb., 2008)] Releasing millions of entries from DDBJ: What has the new computer system in a year brought with? Feb. 1, 2008
In February 2007, DDBJ replaced the computer system and upgraded some of the application programs. In the meantime, DDBJ has been required to process millions of entries. The question here is if the new system has been able to satisfy the emerging requirements.


You might recognize that you can hold your entries in a certain period or until the relevant paper are published. DDBJ should not disclose these Hold-Until-Published entries to the public. To retain them inside DDBJ, DDBJ stores these entries in a separate server from servers for data dissemination, e.g. getentry server.


In the daily data release procedure shown in the following figure, DDBJ convert entries into the flat file format from the server for in-house data management to transfer them to other servers for such services to the public as getentry, ARSA, homology search and anonymous FTP





This month (January 2008), DDBJ released about 1,500,000 entries only in two days; about 1,000,000 entries in the first day, and about 500,000 entries in the second day. It is to be noted that this process was completed as smoothly as designed. With the previous system, we were able to process only 350,000 entries in a day, namely, we had to spend more than 4 days to complete 1.5M entries.


Although the mission was completed this time, we learned some lessons to improve the procedure further. You may claim that "2 days" is not quick enough. The system engineers in charge started the discussion to improve the concordance of several servers to gain higher throughput than ever.


We would appreciate it very much, if you remember the group of hard working system engineers especially when you see the announcement of massive data release.

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

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

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

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

[Databases related to the H-Invitational project]

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

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

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

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

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

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

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

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

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

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

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

Thank you very much for your understanding and cooperation.

[Monthly DDBJ Topic(Jan., 2008)] Releasing millions of entries from DDBJ: What has the new computer system in a year brought with? Feb. 1, 2008
GIB(Genome Information Broker) started the delivery of update information by RSS. You will be notified whenever new genomes are added or existing genomes are updated, if you register the GIB RSS site by use of an RSS reader.

What is RSS?
RSS is a shortened name of Rich Site Summary or Really Simple Syndication, and a number of web site has used to push the information on headline, outline, update date, the link to the web site and so on to the user.
How to read RSS ?
You can subscribe to RSS of any Web site by Google, Yahoo! and other portal sites, if you are a registered user of the portal site. Please find the example of subscription in the following in the case of Goole:
Why you should use RSS?
You need not visit the site every morning to find what's new. You will be notified by the site that the site is updated. In the case of GIB RSS, the list of new genomes and updated genomes is delivered to you. You click the genome of you interest in the list and you are directly guided to the web page of the genome that you choose.
How to register to the GIB RSS
You may want to install a program of RSS reader by yourself, instead of using Google, Yahoo! or other portal sites. We explain the usage of RSS program installed in Windows machine:

  • Install a RSS reader. The following figure is RssReader
  • Register RSS delivery site of GIB(http://gib.genes.nig.ac.jp/rss.php) to the installed RSS reader.
How to register to the GIB RSS
You may want to install a program of RSS reader by yourself, instead of using Google, Yahoo! or other portal sites. We explain the usage of RSS program installed in Windows machine:

  1. Install a RSS reader. The following figure is RssReader(http://www.rssreader.com/)。
  2. Register RSS delivery site of GIB(http://gib.genes.nig.ac.jp/rss.php) to the installed RSS reader.
  3. The line of GIB is added.
  4. Select the GIB line (the box 3 in the figure) and the list from GIB is displayed.
  5. Choose one of the genomes in the list (the box 4 in the figure) and you will know if it is updated or newly added.

Please forward your request to this type of alert system and we will expand RSS to other DDBJ services

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