DDBJ Center News Archive

News from 2011

Release of genome sequence of an uncultivated thermophilic archaeon

2010年12月28日
DDBJ released genome sequence of an uncultivated thermophilic archaeon (Candidatus Caldiarchaeum subterraneum), which had been submitted by the Japan Agency for Marine-Earth Science and Technology.Reference URL: http://www.jamstec.go.jp/e/about/press_release/20101216/The accession numbers (file name for Anonymous FTP download) are as follows;
·AB201309·AP011633·AP011650·AP011675·AP011689·AP011708·AP011723·AP011724·AP011727·AP011745·AP011751·AP011786·AP011796·AP011826 - AP011902
Services: ddbj Keywords: Announcement

Movie manual "How to transfer run data to the DRA" (Japanese)

December 27,2010
Services: dra Keywords:

DDBJ Rel. 84 Completed

December 22,2010
Services: ddbj Keywords: Announcement

DDBJ will terminate accepting submission by 'Sequin'

December 20,2010
DDBJ has accepted nucleotide sequence data submissions by SAKURA, MSS(Mass Submission System), or 'Sequin'. However, DDBJ will terminate accepting submission by 'Sequin' as of the end of January, 2011. Alternatively, by using SAKURA or MSS, you can submit your data easily and quickly by far. Please use SAKURA or MSS hereafter.Please use SAKURA or Mass Submission System (MSS) for your future submission to DDBJ. Reference: Workflow of the data submission to DDBJ(A) SAKURA(B) Mass Submission System (MSS) If you need 'Sequin' submission by unavoidable reason, please send your data to GenBank.Reference: http://www.ncbi.nlm.nih.gov/Sequin/Thank you very much for your understanding and cooperation.
Services: ddbj Keywords: Maintenance

Transcripts induced by salinity stress in rice is released.

December 14,2010
Transcripts induced by salinity stress in rice (Oryza sativa L. ssp. japonica cv. Nipponbare) sequenced by the National Institute of Agrobiological Sciences have been released as DRA000159.
Services: dra Keywords:

Whole genome sequencing data of thermophilic crenarchaeotes is released.

December 14,2010
Whole genome sequencing data of thermophilic crenarchaeotes (Caldiarchaeum subterraneus) sequenced by the Japan Agency for Marine-Earth Science and Technology has been released as DRA000160.
Services: dra Keywords:

Primary whole genome sequencing data of fluoroquinolone-resistant Salmonella enterica is released.

December 03,2010
Primary whole genome sequencing data of fluoroquinolone-resistant Salmonella enterica serovar Typhimurium T000240 sequenced by the National Institute of Technology and Evaluation and the National Institute of Infectious Diseases have been released as DRA000195.
Services: dra Keywords:

DDBJ Sequence Read Archive has released the data search system

November 25,2010
DDBJ Sequence Read Archive has released the data search system (beta). You can search all public data of the DDBJ/EBI/NCBI Sequence Read Archive by accession number, organism name, submitting center name, sequencing platform and study type. Keyword search will be implemented. Metadata is available in XML file and sequencing data can be downloaded in fastq file format. Please try our search system and send us your feedback. For DDBJ/EMBL-Bank/GenBank data, please use getentry and ARSA.DDBJ Sequence Read Archive is a public repository for next-generation sequencing data at primary analysis phase.
Services: ddbj Keywords: Announcement

Metadata XML schema is updated to version 1.2.

November 17,2010
Metadata XML schema is updated to version 1.2. DRA sheet submission is no longer supported. Please submit your metadata by using the MetaDefine or by uploading XML file.
Services: dra Keywords:

BLAST Web API against RefSeq datatabase was opened to the public from WABI

November 09,2010

Following databases of RefSeq has been added to High Speed BLAST API in addition to DDBJ.

Furthermore, Reference proteins (sample program) has been added as a reference database of usual BLAST API.

Use case and execution time

It is possible to do a fast BLAST search against RefSeq databases as well as DDBJ. For example, the following case can be calculated only in a minute. It may change according to whether our server accepts a lot of jobs or not.
Case 1. Comparison between full length cDNA of human and multiple genomes
Sample program can be available here.
Condition:
  • Program: blastn
  • Reference database: Reference genomic sequences (2 million sequences, Total 140 billion bases)
  • Query: Full length cDNA of human gene ALDH2 (DDBJ Accession: BC002967, Sequence length: 2050 bp)
  • Parameter: -b 100 -v 100
Result:Human and a list of homologous species such as horse, dog, chimpanzee, orangutan and rhesus monkey can be obtained. Furthermore, chromosome number and the position on it of their genome or whole genome shotgun can also be obtained.
Case 2. Comparison between environmental DNA sequence and multiple genome
Sample program can be available here.
Condition:
  • Program: blastn
  • Reference database: Reference genomic sequences (2 million sequences, Total 140 billion bases)
  • Query: Environmental DNA sequence (DDBJ Accession: HQ188503, Sequence length: 508 bp)
  • Parameter: -b 100 -v 100 -W 28 -X 20 (equivalent to megablast)
Result: A list of the psychrophilic bacterial species of Shewanella genus can be obtained. Furthermore, the homologous region of their genomes can be also obtained. It is verified that those regions are 16S ribosomal RNA by checking annotations of genomes.Please refer to the page for details.
Services: ddbj Keywords: Announcement

RefSeq databases were added in BLAST(WebAPI)

November 02,2010
Following RefSeq databases were added in BLAST(WebAPI) service. Details are Web API services.
  • Reference genomic sequences
  • Reference mRNA sequences
  • Reference protein sequences
Services: ddbj Keywords: Announcement

Input method of organism names on SAKURA changed

November 01,2010
SAKURA is a nucleotide sequence data submission system through the WWW server at DDBJ."Organism Information" page improved. SAKURA organism names input method changed from Oct. 26, 2010. Details are Sequence data submission via SAKURA. And, about the actual input method, please see SAKURA's help page which is shown after you start the submission.
Services: ddbj Keywords: Announcement

Whole genome sequencing data of a Japanese male is released.

October 28,2010
Whole genome sequencing data of a Japanese male sequenced by Center for Genomic Medicine, RIKEN have been released as DRA000222.
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First Japanese whole genome sequencing data are released from the DDBJ Sequence Read Archive

October 28,2010
Center for Genomic Medicine, RIKEN analyzed the whole genome sequence of a Japanese male which had been genotyped by the International HapMap project. As a result, the research group identified over 3 million single nucleotide variations (SNVs), 5,319 deletions smaller than 10 kb as well as 3 million base pairs of novel genome sequences not found in the human reference genome (Press release from RIKEN).DDBJ Sequence Read Archive has released the sequencing data of the Illumina Genome Analyzer II used in this analysis under the accession number DRA000222.
Services: ddbj Keywords: Announcement

NEDO Human full-length cDNA sequencing projects trace data are available.

October 20,2010
A total of 2,445,650 traces determined by the "NEDO Human full-length cDNA sequencing projects" used to construct the human full-length cDNA clones are available.
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Trace data determined by "Human full-length cDNA sequencing projects" are available

October 20,2010
A total of 2,445,650 traces determined by the New Energy and Industrial Technology Development Organization (NEDO) "Human full-length cDNA sequencing projects" used to construct the human full-length cDNA clones are available.These data are available at *DDBJ Trace Archive and NCBI Trace Archive.  TI numbers:    ∙ 2282248605-2282527996    ∙ 2282791904-2284232295    ∙ 2284242226-2284960269    ∙ 2284238627-2284240689    ∙ 2285528775-2285534533  Anonymous FTP:    ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dta/FLJ/*: DDBJ Trace Archive (DTA) is a permanent repository of DNA sequence chromatograms (traces), base calls, and quality estimates for single-pass reads from various large-scale sequencing projects.
Services: ddbj Keywords: Announcement

Release of new kale (Brassica oleracea var. acephala ) EST 119,204 entries

October 19,2010
DDBJ newly released 119,204 entries of EST data derived from kale (Brassica oleracea var. acephala ) , which had been submitted by Kirin Holdings Company, Ltd.The accession numbers (Anonymous FTP)  are as follows ;These entries were released as DDBJ daily updates on October 13, 2010.
Services: ddbj Keywords: Announcement

Request for the re-submit of the BLAST

October 15,2010
Oct. 15, 2010DDBJ asks the users who has executed the BLAST search during the following period to submit again, because the search results returned during might be incorrect. The details are as follows :
  • Period: from Oct. 7, 2010 at 19:00 to Oct. 15, 2010 at 12:30 (JST)
  • Database selection: "16S rRNA"
At present, the BLAST works normally. We apologize for your inconvenience.
Services: ddbj Keywords: Maintenance

MetaDefine Manual is released from the DRA and MetaDefine movie is released from the DBCLS

September 30,2010
MetaDefine Manual is released from the DRA and MetaDefine movie is released from the DBCLS
Services: dra Keywords:

Forthcoming specification changes around template usage on SAKURA

September 30,2010
SAKURA is a nucleotide sequence data submission system through the WWW server at DDBJ. SAKURA has been open to public and continuously refined since 1995.Since specifications around input items for "Organism Information" page will be improved, DDBJ has to clean up old templates on SAKURA. Details are as follows:
  1.removing template
We will remove all saved templates from SAKURA server at the following schedule. After the removal, you cannot use your previous templates. So, please backup inputs of your templates in the meantime, if necessary.

October 26, 2010     around 9:00AM (JST)
  2.The period of template retention will be changed to 6 months
After 6 months from making, your template will be automatically removed from SAKURA server.
This change will be implemented without the service suspension. Please refer to the SAKURA's help page after it changes for a new input method.Thank you for your understanding and cooperation.
Services: ddbj Keywords: Announcement

DDBJ Rel. 83 Completed

September 22,2010
* 124,079,491 entries: 117,728,717,442 bases * DDBJ Release Note(Rel.83) * Latest Release Information * DDBJ·DAD Release/daily-update FASTA format change * According to the Agreement of the 23rd International Collaborative Meeting, held in this May, The DDBJ/EMBL/GenBank Feature Table: Definition will be revised by the next release issue.
Services: ddbj Keywords: Announcement

DDBJ·DAD Release/daily-update FASTA format change

September 16,2010
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public as the "DDBJ/DAD periodical releases". Moreover, updated data after the cutoff date of the periodical release are released as "ddbjnew/dadnew" every day.The FASTA format for the DDBJ/DAD periodical and daily update is changed. The details are as followsChanged Data (These are available at anonymous FTP)
Data TypeChangeCoverage
ddbjnew/fastaUpper-case letters → Lower-case lettersDDBJ Rel.83 and
DDBJNEW issued after DDBJ Rel.83 cutoff date
ddbjnew/cdsdbRemoval of "//" from the end of the entry
dadnew/fasta
Change in the Services
DatabaseChangeCoverage
getentry
DNA database
CDS amino acid seq FASTARemoval of "//" from the end of the entryDDBJ Rel.83 and
DDBJNEW issued after DDBJ Rel.83 cutoff date
CDS nt seq FASTA
PROTEIN database
amino acid seq FASTARemoval of "//" from the end of the entryDDBJ Rel.83 and
DDBJNEW issued after DDBJ Rel.83 cutoff date
nt seq FASTA (for DAD)
 
supernig
ddbj, ddbjnew/fastaUpper-case letters → Lower-case lettersDDBJ periodical release
dad/fastaRemoval of "//" from the end of the entryDAD periodical release
Services: ddbj Keywords: Announcement

BLAST upgraded

September 02,2010
BLAST (by WWW) have been upgraded from Ver. 2.2.18 to Ver. 2.2.24.(WABI is Sep. 3 upgrade.)
Services: ddbj Keywords: Maintenance

The Report for the 23rd International Collaborators Meeting

September 02,2010
International Nucleotide Sequence Database Collaboration (INSDC), consisted of DDBJ, EBI and NCBI, hold the international collaborators meeting every year.In 2010, the meeting was held at EBI in UK, 19-21 May, to discuss practical matters to maintain and update nucleotide sequence data archives; DDBJ, EMBL-Bank, GenBank, Sequence Read Archive and Trace Archive. As a result of travel disruptions relating to the Icelandic volcano, the meeting was shorter than expected. Despite these difficulties, we believe that we made significant progress at the meeting. The outcomes of the meeting are summarized here.
Services: ddbj Keywords: Announcement

Request for the re-submit of the BLAST

September 02,2010
DDBJ asks the users who has executed the BLAST search during the following period to submit again, because the search results returned during might be incorrect. The details are as follows :
  • Period: from Aug. 17, 2010 at 9:00 to Aug. 27, 2010 at 13:00 (JST)
  • Database selection: "16S rRNA"
At present, the BLAST works normally. We apologize for your inconvenience.
Services: ddbj Keywords: Maintenance

Patent was added to the BLAST protein search

August 27,2010
DDBJ added patent data to the protein data base of BLAST on August 24, 2010. Japan Patent Office (JPO), Korean Intellectual Property Office (KIPO), United States Patent and Trademark office (USPTO) and European Patent Office (EPO) can be selected. The update is scheduled about four times a year.patent
 
Services: ddbj Keywords: Announcement

The NCBI RefSeq data was released in the mirror

August 23,2010
DDBJ has started to mirror the NCBI RefSeq data from August 23, 2010.You can download the RefSeq data from DDBJ's Anonymous-FTP site (ftp://ftp.ddbj.nig.ac.jp/mirror_database/refseq/release/).The directory hierarchy under "/release" is the same as that of NCBI.. The update is scheduled about twice times a month.
Services: ddbj Keywords: Announcement

NIG supercomputer (supernig) services temporary down

August 02,2010
NIG supercomputer (supernig) service will be stopped as following schedule for system maintenance.Date: Aug. 10, 2010 at 9:00 - Aug. 11 at 20:00 (JST)(can not access Supernig system above date)
Thank you for your cooperation.
Services: ddbj Keywords: Maintenance

Release of new fission yeast GSS 113,551 entries and EST 101,079 entries

July 28,2010
DDBJ newly released GSS: 113,551 entries and EST: 101,079 entries derived from fission yeast (Schizosaccharomyces pombe ), which had been submitted by Osaka City University.The accession numbers  (Anonymous FTP)  are as follows ;These entries were released as DDBJ daily updates on Jul. 28, 2010.(Photo: Integrated Database Project)
 
Services: ddbj Keywords: Announcement

DDBJ Sequence Read Archive new name

July 16,2010
DDBJ/EBI/NCBI collaboratively archive raw sequencing data from next-generation sequencers. We have decided to call this international activity as "Sequence Read Archive". According to this, we have changed our database name from "DDBJ Read Archive" to "DDBJ Sequence Read Archive".
 
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Name of database is changed from "DDBJ Read Archive" to "DDBJ Sequence Read Archive" (DRA)

July 14,2010
Name of database is changed from "DDBJ Read Archive" to "DDBJ Sequence Read Archive" (DRA)
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DAD (DDBJ amino acid database) Rel. 52.0 Released

July 13,2010
Future DAD release schedules
  • DDBJ will make up its periodical release 53 in September 2010 as usual. Though we had informed "DAD periodical release 53 would be prepared in December 2010" in the previous release note, we reconsidered to take back the schedule of DAD periodical releases. We apologize for the confusion.
Services: ddbj Keywords: Announcement

ARSA database search (DDBJ, DAD) temporary unavailable

July 09,2010
ARSA is a high-speed data retrieval system provided by DDBJ via WWW and Web API. DDBJ and DAD database search in ARSA is unavailable in the following schedule to update each of released data (DDBJ Release 82.0, DAD Release 52.0 will be released on July 13, 2010.) Details are as follows:
  • Date & Time:  Jul. 16, 2010 (Fri) 9:00 - 18:00 JST (We will announce on this page when the service resumes)
  • Unavailable services:  DDBJ and DAD search in ARSA (another 17DBs are searchable. Search results do not contain DDBJ and DAD entries)  ARSA reference function in TX Search  DNA/Protein/AllDBs search at the search box of the upper part of DDBJ HP (another DB search are available)
Thank you for your understanding and cooperation.
Maintenance works finished. Thank you for your cooperation. (Jul. 16, 2010 at 17:30)
Services: ddbj Keywords: Maintenance

DRA has started to distribute public data of DRA/ERA/SRA

July 07,2010
DDBJ Read Archive (DRA) collects and distributes raw output data from next-generation sequencers with NCBI Sequence Read Archive and EBI Sequence Read Archive.You can download the metadata XML and fastq files released from DRA/ERA/SRA at DRA Download (FASTQ) site.
Services: ddbj Keywords: Announcement

Request for the re-submit of the BLAST

June 30,2010
DDBJ asks the users who has executed the BLAST search during the following period to submit again, because the search results returned during the period might be incorrect. The details are as follows :
  • Period: from June 22, 2010 at 20:00 to June 23, 2010 at 16:30 (JST)
  • Database selection: "DDBJ ALL (DDBJ periodical release + daily updates)"
  • Cause: error in the data update works
At present, the BLAST works normally. We apologize for your inconvenience.
Services: ddbj Keywords: Maintenance

DDBJ Rel. 82 Completed

June 28,2010
Future DDBJ release schedule
  • DDBJ will make up its periodical release 83 in September 2010 as usual. Though we had informed "DDBJ periodical release 83 would be prepared in December 2010" in the previous release note, we reconsidered to take back the schedule of DDBJ periodical releases. We apologize for the confusion.
Services: ddbj Keywords: Announcement

Termination of DDBJ-XML output format

June 25,2010

Termination of DDBJ-XML output format

DDBJ-XML is one of the data output formats, which DDBJ designed based on XML. DDBJ discontinues providing DDBJ-XML data on Jun. 25, 2010. The details are as follows. We apologize for your inconvenience. Thank you for your understanding and cooperation. Termination schedule: Jun. 25, 2010
ServicesTermination
DDBJ periodical releaseDDBJ new dataDDBJ-XML format of Anonymous-FTP
getentryDDBJ-XML format of retrieval result of web, E-mail and FTP data
WABIgetXML_DDBJEntry of GetEntrygetXMLEntry of DDBJ
 The conversion tool is provided. The details are as follows:  tool: ftp://ftp.ddbj.nig.ac.jp/ddbj-cib/tools/DDBJXML/ddbjff2ddbjxml.pl  DTD: ftp://ftp.ddbj.nig.ac.jp/ddbj-cib/tools/DDBJXML/DDBJXML.dtd  README: ftp://ftp.ddbj.nig.ac.jp/ddbj-cib/tools/DDBJXML/README  README - DDBJ anonymous FTP: ftp://ftp.ddbj.nig.ac.jp/ddbj_database/README.TXTJun. 25, 2010
 
Services: ddbj Keywords: Maintenance

Release of new mouse (Mus musculus ) embryo small RNAs, MGA 397,593 entries

June 15,2010
DDBJ newly released small RNA sequences, 397,593 entries of MGA data derived from mouse (Mus musculus) embryos, which had been submitted by National Institute of Neuroscience.The accession numbers are as follows:
  • ALAAA0000001-ALAAA0130942 (130,942 entries)
  • ALAAB0000001-ALAAB0116883 (116,883 entries)
  • ALAAC0000001-ALAAC0092019 (92,019 entries)
  • ALAAD0000001-ALAAD0057749 (57,749 entries)
Anonymous FTP: AL_resource_index.html These entries were released as DDBJ daily updates on Jun. 15, 2010.
 
Services: ddbj Keywords: Announcement

You can download the metadata XML and fastq files released from DRA/ERA/SRA at Download (fastq) ftp site

June 04,2010
You can download the metadata XML and fastq files released from DRA/ERA/SRA at Download (fastq) ftp site
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Modification of way of getting the large size search result by getentry

May 24,2010
DDBJ provides "getentry" as an entry retrieval system by accession numbers etc. The released entries are firstly searchable in the getentry (usually, the next day of releasing works operated)So far, the result view of a large entry (over 10 megabyte file size) in the WWW screen might have caused the system instability and the following interruption of the service.To avoid this problem, DDBJ modified the way of "how to get your result".In the improved system, when a result entry is over 10 megabyte, FTP is automatically selected to get the result, even the user specified the WWW option. In case of multiple entries, if there is one entry which is over 10 megabyte, the all entries are by FTP. This modification will also be applied to the entry view from "ARSA search result" and "Homology Search (BLAST) search result".This change will be active from May 25, 2010.DDBJ will continue to enhnance our services. If you have any comments to DDBJ's services, please send it to DDBJ.May 22, 2010
Services: ddbj Keywords: Maintenance

Started Twitter

May 14,2010
DDBJ started "Twitter". We mainly twitter, about hot topics and updated information etc. http://twitter.com/DDBJ_topics
Services: ddbj Keywords: Announcement

DDBJ/EMBL/GenBank Feature Table Definition revised

May 14,2010
Feature Table Definition (FT-Doc) is the common annotation manual among the three banks (DDBJ, EMBL-Bank, GenBank) for the construction of the DDBJ/EMBL/GenBank International Nucleotide Sequence Database. Feature Table Definition was revised in April 2010. Version is 8.3.
Services: ddbj Keywords: Announcement

Suspension of some parts of DDBJ activities during Japanese holidays

April 21,2010
We at DDBJ suspend our business for releasing data and answering all inquiries on April 29, and from May 1 to 5, 8 and 9, 2010. Search and analysis and another WWW services are available. We will resume the normal business from May 10.
Thank you for your understanding and cooperation.
Services: ddbj Keywords: Maintenance

The Chinese Academy of Science professors visited DDBJ

April 16,2010
chinese academy (April 14, 2010) Six professors of The Chinese Academy of Science (CAS) (include Vice President of CAS) visited NIG and CIB-DDBJ Center. And they held a meeting with CIB-DDBJ staff.
 
Services: ddbj Keywords: Announcement

ARSA database search (DDBJ, DAD) temporary unavailable

April 14,2010
ARSA is a high-speed data retrieval system provided by DDBJ via WWW and Web API. DDBJ and DAD database search in ARSA is unavailable in the following schedule for update each of released data (DDBJ Release 81.0, DAD Release 51.0). Details are as follows:
  • Date & Time:  Apr. 23, 2010 (Fri) 9:00 - 18:00 JST (We will announce on this page when the service resumes)
  • Unavailable services:  DDBJ and DAD search in ARSA (another 17DBs are searchable. Search results do not contain DDBJ and DAD entries)  ARSA reference function in TX Search  DNA/Protein/AllDBs search at the search box of the upper part of DDBJ HP (another DB search are available)
Thank you for your understanding and cooperation.
Maintenance works finished. Thank you for your cooperation. (Apr. 23, 2010 at 16:30)
Services: ddbj Keywords: Maintenance

DAD (DDBJ amino acid database) Rel. 51.0 Released

April 12,2010
  • Date: Apr. 9, 2010
  • 16,673,634 entries    4,623,895,321aa (total number of residues)
  • DAD Release Note
  • DAD release continues to include TPA category data, whereas DDBJ periodical release has separated them.
  • Latest Release Information
Future DAD release schedules
  • In accordance with postponement of DDBJ Rel. 83.0 for 3 months, DAD release will be delayed at the same schedule. Therefore, DAD Rel. 53 will also be released in January 2011.
Services: ddbj Keywords: Announcement

Apologies NIG and DDBJ network inaccessible

April 12,2010
NIG and DDBJ network access was not able to be accessed on Apr. 9. Details are as follows:
  • Period: Apr. 9, 2010 around 9:55 - 13:30(JST)
At present, network is normal. We apologize for your inconvenience.
Services: ddbj Keywords: Maintenance

Release of new Koshihikari rice (Oryza sativa Japonica Group, cultivar Koshihikari ) WGS 654,543 entries

April 05,2010
DDBJ newly released 654,543 entries of WGS data and others derived from Koshihikari rice (Oryza sativa Japonica Group, cultivar Koshihikari ), which had been submitted by National Institute of Agrobiological Sciences.The accession numbers  (Anonymous FTP)  are as follows;Reference sites
Services: ddbj Keywords: Announcement

Release of new purple witchweed (Striga hermonthica ) EST 67,814 entries

April 05,2010
DDBJ newly released 67,814 entries of EST data derived from purple witchweed (Striga hermonthica ), which had been submitted by RIKEN.The accession numbers  (Anonymous FTP)  are as follows;Reference URL: Cultivating TomorrowThese entries were released as DDBJ daily updates on Apr. 2, 2010.
Services: ddbj Keywords: Announcement

Apology for the trouble of results view in Homology Search Result Ret

April 02,2010
The Result Retrieiver is a tool for the confirmation of DDBJ's homology search results when you specify "E-mail" as a method for getting the results. In this Result Retriever, a trouble had broken out during the following period. Details are as follows:
  • Period: April 1, 2010 at 9:30 - April 2, 2010 at 12:00 (JST)
  • Situation: The results had not been displayed in the Result Retriever during the above period.
  • Cause: An effect by the works for the termination of some homology search services.
DDBJ deeply apologize for you inconvenience.
Services: ddbj Keywords: Maintenance

Release of new mouse (Mus musculus domesticus ) GSS 122,131 entries

April 01,2010
DDBJ newly released 122,131 entries of GSS data derived from mouse (Mus musculus domesticus ) strain: C57BL/6NCrlCrlj, which had been submitted by RIKEN BioResource Center.The accession numbers  (Anonymous FTP)  are as follows ;Reference URL: DNA BANKThese entries were released as DDBJ daily updates on Apr. 1, 2010.(Photo: Integrated Database Project)
Services: ddbj Keywords: Announcement

Change of UniProt release numbers and release cycle

March 31,2010
DDBJ provides the UniProt database (UniProt, UniProt/Swiss-Prot, UniProt/TrEMBL) by Anonymous FTP download, and through getentry, ARSA, FASTA/BLAST search services. The data are updated periodically according to the UniProt's updates.From the issue of March 23, 2010, UniProt changed the release cycle and release numbers. The details are as follows. Please note that the same numbering scheme was applied to Swiss-Prot and TrEMBL release numbers.
 
        release number formatrelease cycle                        
      current:YYYY_XX4weeks
      past:x.n3weeks
 
where YYYY is the calendar year and XX is a 2-digit number that is incremented for each release of a given year,e.g. 2010_01, 2010_02, etc.Please refer:
Services: ddbj Keywords: Maintenance

The WGS data of Bacillus subtilis subsp. natto str. BEST195 is released as DRA000001

March 26,2010
The WGS data of Bacillus subtilis subsp. natto str. BEST195 is released as DRA000001 from DRA and SRA
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DDBJ Rel. 81 Completed

March 26,2010
Future DDBJ release schedules
Services: ddbj Keywords: Announcement

DRA Submission Manual was updated to v1.3A

March 19,2010
DRA Submission Manual was updated to v1.3A
Services: dra Keywords:

DRA Submission Manual was updated to v1.3

March 18,2010
DRA Submission Manual was updated to v1.3
Services: dra Keywords:

Removal of "KEGG PATHWAY" from ARSA

March 16,2010
DDBJ will remove "KEGG PATHWAY" from searchable databases in ARSA, as of March 31, 2010. DDBJ apologize for your inconvenience, and thank you for your cooperation.
 
Services: ddbj Keywords: Maintenance

Meta-data creation tool "MetaDefine" was released

March 08,2010
Meta-data creation tool "MetaDefine" was released
Services: dra Keywords:

DRA Submission Manual was updated to v1.2

March 08,2010
DRA Submission Manual was updated to v1.2.
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Release of new tomato (Solanum lycopersicum) GSS 93,682 entries

March 03,2010
DDBJ newly released 93,682 entries of GSS data derived from tomato (Solanum lycopersicum), cultivar: Micro-Tom, which had been submitted by University of Tsukuba. The accession numbers (Anonymous FTP)  are as follows ;These entries were released as DDBJ daily updates on Mar. 3, 2010.(Photo: Integrated Database Project)
 
Services: ddbj Keywords: Announcement

JPO and KIPO amino acid sequence data are available by Anonymous FTP

February 26,2010
DDBJ start to distribute amino acid patent data of Japan Patent Office (JPO) and Korean Intellectual Property Office (KIPO), by anonymous FTP from Feb. 26.For more information, please refer README.TXT about the patent data on Anonymous FTP, README.TXT on ddbj_database, and What's New (Feb. 19).
Services: ddbj Keywords: Announcement

NIG and DDBJ network services temporary down

February 25,2010
NIG (National Institute of Genetics) network service will be unavailable at the following schedule because of the network maintenance. DDBJ network service and NIG supercomputer (supernig) service will also be unavailable.
  • Date: Mar. 21(Sun), 2010 at 18:15 - 19:00 (JST)5 minutes interception during the above time
Thank you for your cooperation.
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JPO and KIPO amino acid sequence data are available by Anonymous FTP

February 19,2010
DDBJ starts to distribute amino acid patent data of Japan Patent Office(JPO) and Korean Intellectual Property Office (KIPO), by anonymous FTP, from February 26, 2010. These amino acid patent data has already been released from DDBJ, since 2008. At the FTP site, JPO and KIPO data construct each files/directories. The update frequency schedules almost quarterly. In DDBJ, the nucleotide sequence data of JPO and KIPO has already been released as DDBJ release, which also contains EPO and USPTO data.For more information, please refer README.TXT about the patent data on Anonymous FTP.
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NIG and DDBJ network services temporary down

February 18,2010
DDBJ network services including NIG supercomputer (supernig) will be unavailable at the following schedule because of the electric power outage. Please note that the suspended period depends on the service.
ServicePeriod
- SAKURAMar. 12(Fri) 17:00 - Mar. 15(Mon) 10:00(JST)
- DDBJ network services (excluding SAKURA)- NIG supercomputer (supernig)Mar. 14(Sun) 9:00 - 21:30(JST)
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Release of new mouse (Mus musculus) small RNA MGA 84,606 entries

February 17,2010
DDBJ newly released 84,606 entries of small RNAs, MGA data, derived from mouse (Mus musculus), which had been submitted by Kinki University.The accession numbers are as follows;
  • ANAAA0000001-ANAAA0033164 (33,164 entries)
  • ANAAB0000001-ANAAB0051442 (51,442 entries)
Anonymous FTP: AN_resource_indexRelated site: About Mass sequence Genome for Sequence (MGA) entryThese entries were released as DDBJ daily updates on Feb. 16, 2010. (Photo: Integrated Database Project)
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Homology Search and ClustalW temporary down

February 10,2010
DDBJ's Homology Search and ClustalW services provided via WWW is temporarily unavailable in the following schedule for the system maintenance.
  • Date & Time: Feb. 16, 2010 (Tue.) at 9:00 - 17:00 (JST) (We will announce on this page when it resumes.)
  • Unavailable services:  - Homology Search (FASTA, BLAST, PSI-BLAST, SSEARCH, HMMPFAM)  - ClustalW
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Maintenance works was finished. Thank you for your cooperation.(Feb. 16, 2010 at 17:00 JST)
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Release of new pig (Sus scrofa) EST 82,326 entries

February 04,2010
DDBJ newly released 82,326 entries of EST data derived from pig (Sus scrofa), which had been submitted by National Institute of Agrobiological Sciences. The accession numbers (Anonymous FTP) are as follows ;These entries were released as DDBJ daily updates on Feb. 4, 2010.(Photo: Integrated Database Project)
 
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Termination of a part of DDBJ services

February 03,2010
DDBJ discontinues the following services provided by WWW and by WebAPI, as of the described schedule. We apologize for your inconvenience. Thank you for your understanding and cooperation.
ServicesTerminationscheduleSubst. servicesby DDBJSubst. servicesoutside DDBJ
  FASTA (WWW/WebAPI)2010.3.31Terminatedsupernig *1EBI (WWW),Univ. of Virginia (WWW),KEGG (WWW)
  SSEARCHsupernig *1EBI (WWW),Univ. of Virginia (WWW),JST(WWW Japanese)
  PSI-BLAST NCBI protein blast(WWW), JST (WWW Japanese)
  HMMPFAM Sanger institute (WWW),HMMER (program download)
*1:for domestic users only (application is required, and support is only in Japanese)
February 1, 2010
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The 9th Japan-Korea-China Bioinformatics Training Course (April, 2010 at Shanghai, China)

February 01,2010
"The 9th Japan-Korea-China Bioinformatics Training Course" will be held at the Shanghai, China, in April 19-23, 2008.This course is for the graduate school students and postdoctoral fellows, and all lectures and exercises are given in English. If you are interested to participate in this training course as a trainee, see the details in the site , and apply it.
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NIG and DDBJ network services temporary down

January 20,2010
NIG (National Institute of Genetics) network service will be unavailable at the following schedule because of the signet router maintenance. DDBJ network service and NIG supercomputer (supernig) service will also be unavailable.
  • Date: Jan. 28(Thu), 2010 at 00:00 - 2:00 (JST)15 minutes interception during the above time
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ARSA database search (DDBJ, DAD) temporary unavailable

January 15,2010
ARSA is a high-speed data retrieval system provided by DDBJ via WWW and Web API. DDBJ and DAD database search in ARSA is unavailabel in the following schedule for update each of released data (DDBJ Release 80.0, DAD Release 50.0). Details are as follows:
  • Date & Time: Jan. 22, 2010 (Fri) 09:00 - 18:00 (We will announce on this page when the service resumes)
  • Unavailabel services:  DDBJ and DAD search in ARSA (another 18DBs are searchable. Search results do not contain DDBJ and DAD entries)  ARSA reference function in TX Search  DNA/Protein/AllDBs search at the search box of the upper part of DDBJ HP (another DB search are available)
Thank you for your understanding and cooperation.
Maintenance works finished. Thank you for your cooperation. (Jan. 22, 2009 at 16:30)
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DAD (DDBJ amino acid database) Rel. 50.0 Released

January 15,2010
  • Date: Jan. 14, 2009
  • 16,207,520 entries:    4,480,429,655aa (total number of residues)
  • In the present release, the format of the SOURCE line in DAD flat file has been changed (change of the order of organism name and organelle name, and inclusion of a common name in some of DAD flat files). For details, please refer the DAD Release Note.
  • Latest Release Information
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DRA File Transfer Manual was updated to "DRA Submission Manual"

January 07,2010
DRA File Transfer Manual was updated to "DRA Submission Manual".
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Release of new false killer whale (Pseudorca crassidens) GSS 90,007 entries

January 07,2010
DDBJ newly released 90,007 entries of GSS data derived from false killer whale (Pseudorca crassidens), hich had been submitted by Korea Research Institute of Bioscience and Biotechnology.The accession numbers  (Anonymous FTP)  are as follows ;Reference siteThese entries were released as DDBJ daily updates on Jan. 7, 2010.
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DDBJ/EMBL/GenBank Feature Table Definition revised

January 04,2010
Feature Table Definition(FT-Doc) is the common annotation manual among the three banks(DDBJ, EMBL-Bank, GenBank) for the construction of the DDBJ/EMBL/GenBank International Nucleotide Sequence Database. Following the decision at an International Collaborators Meeting(ICM) held annually in May, this FT-Doc is updated every year. In December 2009, FT-Doc is updated, based on the 22nd International Collaborators Meeting.
 
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