DDBJ Center News Archive

News from 2015

(Correction) Suspension of the DDBJ activity during the New Year Holidays

2015年12月24日

We at DDBJ will temporarily close for the New Year Holidays from December 26(Sat) 2015 to January 3(Sun) 2016.
Please note that DDBJ Nucleotide Sequence Submission System will be unavailable. Schedule is as follows.
NIG Supercomputer and DDBJ network services (except DDBJ Nucleotide Sequence Submission System)
are available during the New Year Holidays.

During this period, DDBJ will continue to receive inquiries from E-mail and "Contact" web form.
But, please note that replies from DDBJ is after the reopening of the office in January, 2016.

DDBJ office closeDec. 26(Sat), 2015 - Jan. 3(Sun), 2016
DDBJ Nucleotide Sequence Submission SystemDec. 25(Fri), 2015 at 17:00
     - Jan. 4(Mon), 2016 at 10:00 (JST)
Data release suspensionDec. 25(Fri), 2015 - Jan. 4(Mon), 2016
Reply for inquiries
(submission, search/analysis, NIG SuperComputer)
Dec. 26(Sat), 2015 - Jan. 3(Sun), 2016
DRA, BioProject, BioSample, JGA Accession No. issueDec. 26(Sat), 2015 - Jan. 3(Sun), 2016

Thank you for your understanding and cooperation.

December 17, 2015

Services: ddbj Keywords: Announcement

Release of transcriptome sequence data of California harvester ant (Pogonomyrmex californicus)

December 22,2015

DDBJ released transcriptome sequence data of California harvester ant (Pogonomyrmex californicus) which had been submitted by Okinawa Institute of Science and Technology Graduate University.

The accession numbers are as follows. They are available on getentry or DRASearch.

TSA: IAAD01000001-IAAD01311730 (IAAD.gz) (311,730 entries)
DRA: DRR048539-DRR048582 (DRA004112)
Services: ddbj Keywords: Data Release

Release of genome and transcriptome sequence data of Taiwan habu (Protobothrops mucrosquamatu)

December 22,2015

DDBJ released genome and transcriptome sequence data of Taiwan habu (Protobothrops mucrosquamatu) which had been submitted by Okinawa Institute of Science and Technology Graduate University.

The accession numbers are as follows. They are available on getentry or DRASearch.

Genome
WGS: BCNE010000001-BCNE011421934 (BCNE.gz) (1,421,934 entries)
DRA: DRR049668, DRR049669 (DRA004189)
Transcriptome
TSA: IAAC01000001-IAAC01112307 (IAAC.gz) (112,307 entries)
DRA: DRR049635-DRR049665 (DRA004186)
Services: ddbj Keywords: Data Release

Updated tools related to Mass Submission System (MSS)

December 16,2015

DDBJ updated tools related to Mass Submission System.

  • Utilities for MSS file Error check (UME) version 1.40 Released
  • Parser version 6.53 Released

See MSS Home in detail.

Services: ddbj Keywords: Announcement

Release of genome sequence data of azuki bean (Vigna angularis var. angularis)

December 09,2015

DDBJ released genome sequence data of azuki bean (Vigna angularis var. angularis cv. Shumari) which had been submitted by National Institute of Agrobiological Sciences.

The accession numbers are as follows. They are available on getentry or DRASearch.

chromosome
AP015034-AP015044 (11 entries)
scaffold
AP015045-AP017294 (2,250 entries)
DRA
DRR031705 (DRA003236)
DRR031878-DRR031883 (DRA003263-DRA003266)
DRR032984-DRR033067 (DRA003467)
Services: ddbj Keywords: Data Release

Report for DDBJ activities in NAR

December 03,2015

DDBJ activities are introduced in the following article appeared in Nucleic Acids Research, Database issue.

"DNA data bank of Japan (DDBJ) progress report"
Jun Mashima, Yuichi Kodama, Takehide Kosuge, Takatomo Fujisawa, Toshiaki Katayama, Hideki Nagasaki, Yoshihiro Okuda, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Yasukazu Nakamura and Toshihisa Takagi
Nucl. Acids Res. (2015) doi: 10.1093/nar/gkv1105

Services: ddbj Keywords: Announcement

(Dec. 10-17) DDBJ network services and NIG Supercomputer will be unavailable (all service resumed)

December 01,2015

DDBJ network services and NIG SuperComputer will be unavailable due to NIG Supercomputer maintenance as follows.

ServicesSchedule (JST)
・DRA validationDec. 10 (Thu) 14:00 - Dec. 17 (Thu) 14:00 (JST)
・MiGAPDec. 10 (Thu) 17:00 - Dec. 17 (Thu) 10:00 (JST)
・D-way
・DRA Search
・BioProject Search
・BioSample Search
・JGA Submission/Download Tool
・JGA Meta Viewer
Dec. 11 (Fri) 13:00 - Dec. 17 (Thu) 9:00 (JST)
・NIG Supercomputer
・DDBJ Read Annotation Pipeline
Dec. 11 (Fri) 17:00 - Dec. 16 (Wed) 24:00 (JST)
・DDBJ anonymous FTP
・getentry
・ARSA
・TXSearch
・BLAST
・ClustalW
・DDBJ Homepage
Dec. 11 (Fri) 17:00 - Dec. 17 (Thu) 9:00 (JST)
・DDBJ Nucleotide Sequence Submission SystemDec. 11 (Fri) 17:00 - Dec. 17 (Thu) 10:00 (JST)

Thank you for your understanding and cooperation.

DDBJ services are available.
Thank you for your cooperation.

DRA validation is unavailable until December 17 (Thu), 14:00 (JST).

Services: ddbj Keywords: Announcement

Downtime of DRA, BioProject and BioSample services due to the NIG super computer maintenance

December 01,2015

From 11, December (Fri.) 13:00 - 17, December (Thu.) 9:00Downtime depends on maintenance schedule of the NIG super computer.

  • D-way
  • DRA Search
  • BioProject Search
  • BioSample Search
  • JGA Submission/Download Tool
  • JGA Meta Viewer

From 10, December (Thu.) 14:00 - 17, December (Thu.) 14:00

  • DRA validation

(Dec. 10-17) DDBJ network services and NIG Supercomputer will be unavailable

Services: bioproject,biosample,gea,dra,dta,jga Keywords: Maintenance

Release of transcriptome sequence data of ayu (Plecoglossus altivelis altivelis)

November 30,2015

DDBJ released transcriptome sequence data of ayu (Plecoglossus altivelis altivelis), which had been submitted by National Research Institute of Aquaculture.

The accession numbers are as follows. They are available on getentry or DRASearch.

tissue TSA DRA Run
thrombocyte LA715952-LA738445 (22,494) DRR024801
neutrophil LA738446-LA761178 (22,733) DRR025094
B lymphocyte LA761179-LA777683 (16,505) DRR024802
Services: ddbj Keywords: Data Release

Release of genome sequence data of Hawaiian acornworm (Ptychodera flava)

November 24,2015

DDBJ released genome sequence data of Hawaiian acornworm (Ptychodera flava) which had been submitted by University of Tsukuba.

The accession numbers are as follows. They are available on getentry or DRASearch.

WGS: BCFJ01000001-BCFJ01317432 (BCFJ.gz) (317,432 entries)
CON: LD342582-LD560836 (218,255 entries)
DRA: DRA002855 (DRR027930-DRR027956)
Services: ddbj Keywords: Data Release

Feature Table Definition revised

November 17,2015

The DDBJ/ENA/GenBank Feature Table Definition is the common annotation manual of feature descriptions for DDBJ, ENA and GenBank.
It was revised to version 10.5.

Services: ddbj Keywords: Announcement

Release of transcriptome sequence data of common house spider (Parasteatoda tepidariorum)

November 13,2015

DDBJ released transcriptome sequence data of common house spider (Parasteatoda tepidariorum), which had been submitted by Keio university.

The accession numbers are as follows. They are available on getentry or DRASearch.

TSA: IAAA01000001-IAAA01132843 (132,843 entries) IAAA.gz
DRA Run: DRR047015-DRR047017

Services: ddbj Keywords: Data Release

Special system maintenance (14:00-16:00, 6 Nov.) [delayed]

November 04,2015
From 14:00 to 16:00 (planned), 6th (Friday), November, the D-way submission and DRA, BioProject and BioSample search services will be unavailable due to special maintenance of hardware.

System restarted.

Services: bioproject,biosample,dra Keywords: Maintenance

System maintenance (9:30-11:30, 4 Nov.)

October 28,2015
From 9:30 to 11:30 (planned), 4th (Wednesday), November, the DRA, BioProject and BioSample submission services will be unavailable due to scheduled maintenance of D-way.
Services: bioproject,biosample,dra Keywords: Maintenance

Release of genome sequence data of Oryza sativa Japonica Group

October 13,2015

DDBJ released genome sequence data of Oryza sativa Japonica Group cv. Nipponbare with the annotaion of the International Rice Genome Sequencing Project which had been submitted by National Institute of Agrobiological Sciences.

Reference
Database: RAP-DB

The accession numbers are as follows. They are available on getentry.

chromosome:
AP014957-AP014968 (12 entries)
unanchored:
AP014969-AP015011 (43 entries)
Services: ddbj Keywords: Data Release

Apologies for DDBJ web services were unavailable

October 09,2015

During the following period, DDBJ web services were unavailable.

Period: October 8 (Thu), 20:56 - October 9 (Fri), 8:47 (JST)

At present, DDBJ web services work normally.
We apologize for the inconvenience.

Services: ddbj Keywords: Maintenance

Apologies for defects in getentry

October 02,2015

getentry system failure has occurred from 05:45 to 9:40 on Oct 2(JST).

getentry is now available.
DDBJ sincerely apologize for your inconvenience.

Services: ddbj Keywords: Announcement

Updated tools related to Mass Submission System (MSS)

October 02,2015

DDBJ updated tools related to Mass Submission System.

  • Utilities for MSS file Error check (UME) version 1.39 Released
  • Parser version 6.52 Released
  • transChecker version 2.19 Released

See MSS Home in detail.

Services: ddbj Keywords: Announcement

DDBJ Rel. 102.0, DAD Rel. 72.0 Completed

September 29,2015

DDBJ Rel. 102.0

DAD (DDBJ amino acid database) Rel. 72.0
  • Date: Sep. 29, 2015
  • 43,653,463 entries     13,562,515,245 aa (total number of residues)
  • DAD Release Note
Services: ddbj Keywords: Data Release

The Report for the 28th International Collaborators Meeting

September 08,2015

International Nucleotide Sequence Database Collaboration (INSDC), consisted of DDBJ, EBI and NCBI, hold the international collaborators meeting every year.
In 2015, tthe meeting was held at NCBI, 19-21 May, to discuss practical matters to maintain and update nucleotide sequence data archives; DDBJ, ENA, GenBank, Sequence Read Archive (SRA) and Trace Archive.
The outcomes of the meeting are summarized here.

Services: ddbj Keywords: Announcement

Apology for the DDBJ service down on September 2

September 03,2015

Due to the electric power outage caused by lightning strike which occurred around 10:20 on September 2, DDBJ services were unavailable.

As of September 3 (Thu), 16:45 (JST), all DDBJ service is available.
DDBJ sincerely apologize for your inconvenience.

Services: ddbj Keywords: Maintenance

(Today) DDBJ network service is unavailable

September 02,2015

DDBJ network service is unavailable because of the electric power outage which occurred on September 2.
Please wait for a while till the restoration.

Thank you for your understanding and cooperation.

Services: ddbj Keywords: Maintenance

Release of genome sequence data of Lotus japonicus

September 01,2015

DDBJ released genome sequence data of Lotus japonicus which had been submitted by Kazusa DNA Research Institute.

Reference
Database: miyakogusa.jp

The accession numbers are as follows. They are available on getentry or DRASearch.

WGS: BABK02000001-BABK02044464 (BABK.gz) (44,464 entries)
CON: DG000091-DG000096 (6 entries)
DRA: DRA001236 (DRR014723-DRR014732)
Services: ddbj Keywords: Data Release

Data release and modified information for Korean Intellectual Property Office (KIPO)

August 21,2015
DDBJ distributed the patent application sequence submitted from Korean Intellectual Property Office (KIPO).
This submission was started transferring RNA data and adding new lines for CC, FH and FT header on Flat file (FF).

1) Accession number (Acc#)
KIPO data was issued the accession number as follows.
Nucleotide sequence (NA) data: DI409117-DI486707 (77,591 entries; DNA data: 47,242 entries, RNA data: 30,349 entries)
Amino acid sequence (AA) data: DI746460-DI792915 (46,456 entries)

Please check the released data by using getentry for Acc# and ARSA for keyword.



2) COMMENT block
COMMENT block was described as follows.
New lines for CC, FH and FT header were added after TY line.
------------------------------------------------------------------------------------------      
Header       Description contents--------------------------------------------------
----------------------------------------COMMENT    KN      Sequence ID            
AN        Application number            AD        Application date            
PN        Publication number            PD        Publication date            
AT        Application title            AI        Inventors (bar-separated)            
AA        Applicants (bar-separated)            
PR        Priority number=Priority date (bar-separated)            
OS        Organism name            TY        Sequence type (DNA, RNA, PRT)            
CC        Comment            FH        Fixed character string of "Key   
Location/Qualifiers"            FT        Feature/qualifier information-------------------
-----------------------------------------------------------------------
(New addition headers)
CC: This line is described as supplemental information for sequence and others. In case of no value, it will be omitted.
FH: This line is described "Key  Location/Qualifiers" as fixed character string. It is mandatory line.
FT: This line is described as feature/qualifier information. In case of no value, it will be omitted.


(RNA data)
RNA data is described as "RNA" on TY line.





3) Collaboration
Submission files were processed and submitted to DDBJ by Dr. Byungwook Lee at Korean Bioinformation Center (KOBIC) in collaboration with KIPO.



Services: ddbj Keywords: Data Release

[DRA] FTP service is available

August 17,2015

FTP service (DRA fastq file) is available.
We apologize for the inconvenience.

Services: ddbj Keywords: Maintenance

Data validation process is suspended due to disk trouble

August 17,2015
Data validation process is suspended due to disk trouble.
Services: bioproject,biosample,dra Keywords:

[DRA] FTP service is unavailable due to disk problem

August 12,2015

At present, FTP service (DRA fastq file) is unavailable due to disk problem.
We apologize for the inconvenience.

Services: ddbj Keywords: Maintenance

Release of genome sequence data of common marmoset (Callithrix jacchus)

August 11,2015

DDBJ released genome sequence data of common marmoset (Callithrix jacchus) which had been submitted by Keio University.

The accession numbers are as follows. They are available on getentry or DRASearch.

WGS: BBXK01000001-BBXK01109198 (BBXK.gz) (109,198 entries)
CON: DG000097-DG000120 (24 entries)
DRA: DRA003594 (DRR036754-DRR036764)
GSS: LB274659-LB427105 (152,447 entries)
Services: ddbj Keywords: Data Release

(8/13-14) Suspension of some parts of DDBJ activities during Summer Holidays

August 03,2015

DDBJ will suspend our business on releasing data and answering inquiries from August 13 to August 14, 2015(JST) due to NIG Summer Holidays. We will reply to your messages on or after August 17. But, all WWW services are available.

    Thursday, August 13, 2015 - Friday, August 14, 2015 (JST)

Thank you for your understanding and cooperation.

Services: ddbj Keywords: Announcement

Scheduled maintenance (9:30-11:30, 5 Aug.)

July 29,2015
From 9:30 to 11:30 (planned), 5th, August, the DRA, BioProject and BioSample submission and search services will be unavailable due to scheduled maintenance.
Services: bioproject,biosample,dra Keywords: Maintenance

Release of genome and transcriptome sequence data of soybean (Glycine max cv. Enrei)

July 21,2015

DDBJ released genome and transcriptome sequence data of soybean (Glycine max cv. Enrei) which had been submitted by National Institute of Agrobiological Sciences.

The accession numbers are as follows. They are available on getentry or DRASearch.

Genome
WGS: BBNX02000001-BBNX02108601 (BBNX.gz) (108,601 entries)
DRA: DRA002416 (DRR021740-DRR021744)
Transcriptome
DRA: DRA003212 (DRR031435)
Services: ddbj Keywords: Data Release

Services are now available

July 02,2015
Although the submission and search services for DRA, BioProject, and BioSample were temporarily unavailable due to hardware troubles, these services are now available. We apologize for the inconvenience.
Services: bioproject,biosample,dra,dta Keywords:

Submission system and search services are unavalilable

July 02,2015
DRA, BioProject and BioSample submission and search services are temporarily unavailable due to hardware troubles. If restored, we will announce.
Services: bioproject,biosample,dra,dta Keywords:

(Jul. 7 - Jul. 14) JGA services are unavailable

June 29,2015
Services: jga Keywords: Maintenance

DDBJ Rel. 101.0, DAD Rel. 71.0 Completed

June 24,2015

DDBJ Rel. 101.0

DAD (DDBJ amino acid database) Rel. 71.0
  • Date: Jun. 24, 2015
  • 41,675,650 entries     12,913,734,732 aa (total number of residues)
  • DAD Release Note
Services: ddbj Keywords: Data Release

(Jul. 7 – Jul. 13) DDBJ services and NIG Supercomputer will be unavailable

June 23,2015
Services: bioproject,biosample,gea,dra,dta Keywords: Maintenance

(Jul. 7 - Jul. 13) DDBJ services and NIG Supercomputer will be unavailable (all service resumed)

June 23,2015

DDBJ services and NIG Supercomputer will be unavailable due to NIG Supercomputer maintenance as follows.

ServicesSchedule (JST)
・D-way
・DRA Search
・BioProject Search
・BioSample Search
Jul. 7 (Tue) 13:00 ~ Jul. 13 (Mon) 10:00 (JST)
・JGA Submission/Download Tool
・JGA Meta Viewer
Jul. 7 (Tue) 13:00 ~ Jul. 14 (Tue) 10:00 (JST)
・NIG SuperComputerJul. 8 (Wed) 9:00 ~ Jul. 11 (Sat) 24:00 (JST)
・DDBJ anonymous FTP
・getentry
・ARSA
・DDBJ Nucleotide Sequence Submission System
・TXSearch
・BLAST
・ClustalW
・DDBJ Read Annotation Pipeline
・MiGAP
・DDBJ Homepage
Jul. 8 (Wed) 9:00 ~ Jul. 13 (Mon) 10:00 (JST)

Thank you for your understanding and cooperation.

DDBJ services are available.
Thank you for your cooperation.

JGA service is unavailable until July 14 (Tue), 10:00 (JST).

Services: ddbj Keywords: Maintenance

Release of genome and transcriptome sequence data of radish (Raphanus sativus cv. Aokubi)

June 10,2015

DDBJ released genome and transcriptome sequence data of radish (Raphanus sativus cv. Aokubi) which had been submitted by Tokyo University of Agriculture.

Reference;
Database: NODAI Radish genome database

The accession numbers are as follows. They are available on getentry or DRASearch.

Genome sequence

scaffold CON: DF196826-DF236948 (40,123 entries)
WGS: BAOO01000001-BAOO01072909 (BAOO.gz) (72,909 entries)

DRA: DRA001016

Transcriptome sequence

DRA: DRA001003

Services: ddbj Keywords: Data Release

27th, May, system maintenance

May 15,2015
From 14:00-17:00, 27th, May, the JGA submission/download tools and metadata viewer will not be available due to system maintenance.
Services: jga Keywords: Maintenance

Release of transcriptome sequence data of Hokkaido salamander (Hynobius retardatus)

April 30,2015

DDBJ released transcriptome sequence data of Hokkaido salamander (Hynobius retardatus), which had been submitted by Hokkaido University.

The accession numbers are as follows. They are available on getentry or DRASearch.

TSA: LE000001-LE740933 (740,933 entries)
DRA Run: DRR016729-DRR016800

Services: ddbj Keywords: Data Release

Web services will be unavailable (24th, Apr. 9:30-10:30)

April 23,2015
Due to system maintenance, web services (search and D-way submission services) will be unavailable (24th, Apr. 9:30-10:30).
Services: bioproject,biosample,dra,dta Keywords: Maintenance

Attention for alphabetical sorting of BioSamples submitted from D-way

April 23,2015

After submitting BioSamples from D-way, BioSamples are sorted in alphabetical (ASCII code) order of sample_name values and NOT in order of appearance (top to bottom in tab-delimited text file). BioSample accession numbers are issued to the alphabetically-sorted BioSamples.

Please enter sample_name values as such their "order of appearance" and "alphabetical order" to be same.

Since the sample_name is used as the identifier in database system, it cannot be changed after submission. Submitters can name sample by using the sample_title attribute. The sample_title is used as a title in public record and can be updated.

sample_names contain serial numbers

Following samples are sorted as intended.

0001_control
0002_a sample
0003_b sample

Following examples are NOT sorted as intended (sorted by first letters).

1_control
5_a sample
10_b sample
->
1_control
10_b sample
5_a sample

DDBJ is developing the database system to preserve order of appearance (top to bottom in tab-delimited text file). If you have questions, please contact us from here.

Services: bioproject,biosample,dra Keywords: Announcement

Suspension of some parts of DDBJ activities during Japanese national holidays

April 21,2015

We at DDBJ will temporarily close for the Japanese National Holidays April 29 and from May 2 to May 6, 2015.
NIG SuperComputer and DDBJ network services are available during the holidays.
We will resume the normal business from May 7, 2015.

During this period, DDBJ will continue to receive inquiries from E-mail and "Contact" web form.
But, please note that replies from DDBJ is after the reopening of the office in May 7, 2015.

Thank you for your understanding and cooperation.

Services: ddbj Keywords: Announcement

Release of transcriptome sequence data of common iceplant (Mesembryanthemum crystallinum)

April 06,2015

DDBJ released transcriptome sequence data of common iceplant (Mesembryanthemum crystallinum), which had been submitted by Nagoya University.

The accession numbers are as follows. They are available on getentry or DRASearch.

TSA: FX891461-FX944976 (53,516 entries)
DRA Run: DRR018522-DRR018525

Services: ddbj Keywords: Data Release

Release of genome sequence data of a species closely related to sweet potato (Ipomoea trifida)

April 01,2015

DDBJ released genome sequence data of two cultivars of a species closely related to sweet potato (Ipomoea trifida), which had been submitted by Kazusa DNA Research Institute.

Reference;
Sweetpotato GARDEN

The accession numbers are as follows. They are available on getentry or DRASearch.

Ipomoea trifida cultivar Mx23Hm
    scaffold CON: DF850533-DF884990 (34,458 entries)
    WGS: BBOG01000001-BBOG01163047 (BBOG.gz) (163,047 entries)
    DRA run: DRR023905-DRR023907

Ipomoea trifida cultivar 0431-1
    scaffold CON: DF884991-DF933566 (48,576 entries)
    WGS: BBOH01000001-BBOH01377770 (BBOH.gz) (377,770 entries)
    DRA run: DRR023898-DRR023904

Services: ddbj Keywords: Data Release

Release of genome sequence data of tadpole shrimp (Triops cancriformis)

April 01,2015

DDBJ released genome sequence data of tadpole shrimp (Triops cancriformis), which had been submitted by Keio University.

The accession numbers are as follows. They are available on getentry or DRASearch.

WGS: BAYF01000001-BAYF01060629 (BAYF.gz) (60,629 entries)
DRA run: DRR017999

Services: ddbj Keywords: Data Release

8th, April, BioProject/BioSample/DRA wer services maintenance

March 30,2015
Due to system update, the BioProject/BioSample/DRA web services will be unavailable during 9:30-14:00, 8th, April (Wed).Web services: D-way, DRA Search, BioProject Search and BioSample SearchData validation process will be unavailable during 7th 17:30 - 8 th 14:00, April.
Services: bioproject,biosample,dra,dta Keywords: Maintenance

DDBJ Rel. 100.0, DAD Rel. 70.0 Completed

March 25,2015

DDBJ Rel. 100.0

DAD (DDBJ amino acid database) Rel. 70.0
  • Date: Mar. 25, 2015
  • 39,229,464 entries     12,028,089,596 aa (total number of residues)
  • DAD Release Note
Services: ddbj Keywords: Data Release

Part of ftp and DRA search services are unavailable

March 25,2015
Due to hardware troubles, ftp directories under the following path are not accessible.ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/
In the DRA search, keyword search, bases and qualities display functions are not available.
Services: bioproject,biosample,gea,dra,dta Keywords: Maintenance

(Mar. 17) ARSA temporarily unavailable (Resumed)

March 13,2015

ARSA will be unavailable due to NIG SuperComputer maintenance as follows.

 March 17 (Tue), 16:00 - 19:00 (JST)

Thank you for your understanding and cooperation.

NIG SuperComputer maintenance finished. ARSA is available. (March 17, 2015 at 18:00 JST)
Thank you for your cooperation.

Services: ddbj Keywords: Announcement

Users are able to submit BioProject/BioSample/DRA at once

March 11,2015

New BioProject, BioSample and DRA submission system were released at 8th, April (Wed).

This system enhancement was carried out by funding from MEXT Genome Science.

Tutorial video.[youtube id="Hg4h8ytbIV4" title="Submission to BioProject, BioSample and DRA"]

DRA Handbook

The new system is able to reference and submit BioProject, BioSample and DRA submissions which had been registered in the former system.

BioProject, BioSample and DRA data can be submitted at once

Before submission to DRA, BioProject and BioSample accession numbers were required.In the new system, BioProject, BioSample and DRA data can be submitted at once, so submitters need not to wait for BioProject and BioSample accession numbers.

Experiment and Run which are same number of BioSample, are automatically created.Submitter and hold action in the DRA submission are copied to "SUBMITTER" of BioProject and BioSample.

BioProject and DRA data can be submitted at once
BioSample and DRA data can be submitted at once

Registered BioSample attributes text file is available in D-way

Users can download the registered BioSample attributes text file in D-way (blue box).Updates will be reflected to the file.

Download sample attribute file

Reference sequence of bam can be specified by accession number

Reference sequence in single fasta file was required to submit alignment data in bam.

In the new system, if references are found in ftp://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/,references can be specified by their accession numbers.

In the DRA submission tool, "BioSample Used" was moved

In the DRA submission tool, "BioSample Used" was moved from rightmost to just right to "Experiment Alias",which enables users to easily understand relationship between "Experiment" and "referencing BioSample".

BioSample Used is moved to just right to Experiment Alias

Fastq from capillary sequencing platforms can be submitted to DRA

In the DRA submission tool, capillary sequencing platforms can be selected.Fastq from these platforms can be submitted to DRA.To submit sequence chromatgrams, please continue to submit data to DDBJ Trace Archive.

  • AB 3730xL Genetic Analyzer
  • AB 3730 Genetic Analyzer
  • AB 3500xL Genetic Analyzer
  • AB 3500 Genetic Analyzer
  • AB 3130xL Genetic Analyzer
  • AB 3130 Genetic Analyzer
  • AB 310 Genetic Analyzer

Sequencing instruments were added

In the DRA submission tool, following Illumina and Oxford nanopore sequencers were added.

  • HiSeq X Ten
  • NextSeq 500
  • MinION
  • GridION

PacBio hdf5 file can be submitted

PacBio hdf5 file can be submitted.Select "PacBio_HDF5" for Run File Type.

"Illumina_native", "Illumina_native_qseq" and "Helicos_native" are removed from Run filetype

"Illumina_native", "Illumina_native_qseq" and "Helicos_native" are removed from Run filetype. These types can be specified in XML.

Other changes

  • BioProjectand BioSample Submitting organizations are pre-entered with "Lab/Group", "Department (2)", "Department (1)", "Organization" of D-way account.Text in the submitting organization can be editted.
  • BioSample "Private comments to DDBJ staff" was moved from "COMMENTS" tab to "GENERAL INFO". "COMMENTS" tab was removed.
Services: bioproject,biosample,dra Keywords: Announcement

Release of genome sequence data of Antarctic minke whale (Balaenoptera bonaerensis)

February 23,2015

DDBJ released genome sequence data of Antarctic minke whale (Balaenoptera bonaerensis), which had been submitted by Kyoto University.

The accession numbers are as follows. They are available on getentry or DRASearch.

scaffold CON: DF397027-DF818470 (421,444 entries)
WGS: BAUQ01000001-BAUQ01720900 (BAUQ.gz) (720,900 entries)
DRA run: DRR014695

Services: ddbj Keywords: Data Release

FANTOM5 phase 2 data released

February 17,2015

At 13rd, February, DDBJ Sequence Read Archive released FANTOM5 Phase2 data submitted by RIKEN.
The FANTOM5 phase 2 project examined 19 human cell types and 14 mouse cell types undergoing a variety of cellular changes, showed that it is the activation of enhancers that triggers the coordinated waves of change that end up dramatically changing the phenotypes of the cells.

Accession numbers
DRA000991
DRA002711
DRA002747
DRA002748

Press release by RIKEN
RIKEN & FANTOM consortium, "Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.", Science, doi: 10.1126/science.1259418

Services: ddbj Keywords: Data Release

Updated tools related to Mass Submission System (MSS)

February 13,2015

DDBJ updated tools related to Mass Submission System.

  • Utilities for MSS file Error check (UME) version 1.38 Released
  • Parser version 6.51 Released
  • transChecker version 2.18 Released

See MSS Home in detail.

Services: ddbj Keywords: Announcement

Release of transcriptome sequence data of welsh onion (Allium fistulosum)

February 05,2015

DDBJ released transcriptome sequence data of welsh onion (Allium fistulosum), which had been submitted by Institute of Vegetables and Tea Science.

The accession numbers are as follows. They are available on getentry or DRASearch.

TSA: FX553726-FX608587,FX657476-FX657516 (54,903 entries)
DRA run: DRR006298-DRR006306

Services: ddbj Keywords: Data Release

(Jan. 27) ARSA temporarily unavailable (Resumed)

January 26,2015

ARSA will be unavailable due to NIG Supercomputer maintenance as follows.

 January 27 (Tue), 14:00 - 17:00 (JST)

Thank you for your understanding and cooperation.

NIG Supercomputer maintenance finished. ARSA is available. (January 27, 2015 at 16:00 JST)
Thank you for your cooperation.

Services: ddbj Keywords: Maintenance

Nucleotide Sequence Submission System (NSSS) Updated

January 15,2015

DDBJ Nucleotide Sequence Submission System (NSSS) updated.
Due to the system updated, "6. Template" and "7. Annotation" page design and function have been improved.

 (Jan. 15) Important Notification regarding Nucleotide Sequence Submission System (NSSS)

Services: ddbj Keywords: Announcement

Release of genome sequencing data of STAP-related cell lines

January 15,2015

DDBJ center released genome sequencing data of STAP-related cell lines, which had been submitted by RIKEN. Press release by RIKEN (Japanese)

The accession number is as follows.

DRA002862

Services: ddbj Keywords: Data Release

Scheduled maintenance (9:30-12:00, 14 Jan.)

January 08,2015
From 9:30 to 12:00, Wednesday, 14th, January, the DRA, BioProject and BioSample submission and search services will be unavailable due to scheduled maintenance.
Services: bioproject,biosample,dra,dta Keywords: Maintenance

(Jan. 6) ARSA temporarily unavailable (Resumed)

January 06,2015

ARSA will be unavailable due to NIG Supercomputer maintenance as follows.

 January 6 (Tue), 13:00 - 16:00 (JST)

Thank you for your understanding and cooperation.

NIG Supercomputer maintenance finished. ARSA is available. (January 6, 2015 at 15:10 JST)
Thank you for your cooperation.

Services: ddbj Keywords: Maintenance
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