DDBJ » DDBJ NEWS/English

(May 17-20) Some functions of DDBJ services are unavailable(all service resumed)

jukohira — Mon, 13 May 2013 02:31:00 +0000

Some functions of DDBJ services will be unavailable at the following schedule because of the NIG(National Institute of Genetics) network system maintenance.

All Services and functions are resumed. DDBJ apologizes for your inconvenience. (May 21 11:50(JST)).

Services	Unavailable functions	Period
DDBJ Home Page	Submission of inquiries Mass Submission System application	May 17 (Fri) 18:00 (JST) - May 18 (Sat) 09:00 (JST)
DDBJ Sequence Read Archive DDBJ Trace Archive DDBJ BioProject	Creating D-way submission account Data Submission·Update (via D-way) Data Search	May 17 (Fri) 15:00 (JST) -
getentry ARSA	Data release Data update	May 17 (Fri) 15:00 (JST) - May 20 (Mon) 12:00 (JST) deferred data will be released/updatted after the service resumption
FTP	Data download Data release·update	May 18 (Sat) 15:00 (JST) -

Thank you for your cooperation and understanding.

May 13, 2013

DDBJ Web Magazine-e April 2013 Issue

fhirata — Thu, 25 Apr 2013 05:45:08 +0000

April 2013 Issue Apr. 25, 2013

Suspension of some parts of DDBJ activities during Japanese holidays

Enhancement in DDBJ BLAST

Release of sequence data from DDBJ (Apr. 2013)

New COMMENT format for Japan Patent Office (JPO) data

"FAQ of DDBJ Nucleotide Sequence Submission System" -Vol.2

Release of genome sequence data of mouse (Mus musculus strain MSM/Ms)

fhirata — Fri, 19 Apr 2013 05:43:04 +0000

DDBJ released genome sequence data of mouse (Mus musculus strain MSM/Ms), which had been submitted by National Institute of Genetics.

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

WGS: BAAG010000001-BAAG011237600 (BAAG.gz) (1,237,600 entries)

Release of genome sequence data of a biofuel crop, Jatropha curcas

fhirata — Mon, 15 Apr 2013 05:26:10 +0000

DDBJ released genome sequence data of a biofuel crop, Jatropha curcas, which had been submitted by the Kazusa DNA Research Institute.

The sequence data are updated version of previously released one.

Reference URL;

    Jatoropha database

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

    scaffold CON: DF145383-DF157092 (11,710 entries)
    WGS: BABX02000001-BABX02066610 (BABX.gz) (66,610 entries)
    raw data: DRR001794, DRR001795

DDBJ services temporary unstable due to network failure

jukohira — Thu, 04 Apr 2013 08:50:06 +0000

Because of the network system failure, some DDBJ services are temporary unstable connection.

Recovery works are in operation. We will announce on this page as soon as the maintenance are completed.

Thank you very much for your understanding and cooperation.

System failure was resolved, and DDBJ services operates normally.
We apologize for you inconvenience. (at 9:00 Apr. 5, 2013(JST))

Enhancement in DDBJ BLAST

jukohira — Tue, 02 Apr 2013 06:40:54 +0000

DDBJ greatly improved the homology search BLAST.

Selections of Data Sets and Divisions were modified
Get the result by E-mail, as well as in the web screen
Direct link to the flat file of the corresponding accession number
Link-up to ClustalW
Request ID was not included in the URL of the result
New function Result Viewer was equipped

Selections of Data Sets and Divisions were modifi

(1) Datasets are selected from DDBJ ALL, DDBJ New, 16SrRNA (in case of nucleotide)
(2) In the specification of Divisions, you can select general classifications (Standard divisions, High thryoughput divisions, EST divisions , Other divisions), and detailed specification of divisions are available.

get the result by E-mail, as well as web screen

You can select the method of getting the result either E-mail or WWW.

direct link to the flat file of the corresponding accession number

You can view the flatfile of the sequences in the getentry.

Request ID was not included in the URL of the result

After pressing the "Send to BLAST" button, Request ID is displayed on the web screen. Don't loose this ID because it is necessary for using the "Result Viewer" and/or inquiring to DDBJ for your search.

New function Result Viewer

You can view your result using "Request ID" at any time (within the retention period).

Link-up to ClustalW

Select the sequences which you would like to suceed the clustalW, then press the "ClustalW" button. Your selected sequences are automatically pasted in the ClustalW query box.

DDBJ will continue to improve the services. Your revies and comments will be helpful for DDBJ's improvement. Please send your comments from "Contact Us" page. (Please select the item "Web Support ")

Release of EST data of white-tufted-ear marmoset (Callithrix jacchus)

jmashima — Tue, 02 Apr 2013 01:38:29 +0000

DDBJ released 5'-EST data derived from white-tufted-ear marmoset (Callithrix jacchus), which had been submitted by National Institute of Genetics.

The accession numbers are as follows. (Available by getentry)

EST: HX373156-HX663542 (290,387 entries)

DDBJ Rel. 92.0, DAD (DDBJ amino acid database) Rel. 62.0 Completed

fhirata — Thu, 21 Mar 2013 02:34:32 +0000

DDBJ Rel. 92.0

Date:Mar. 21, 2013
163,017,305 entries 150,760,062,903 bases
DDBJ Release Note
Latest Release Information

DAD (DDBJ amino acid database) Rel. 62.0

Date: Mar. 21, 2013
26,351,045 entries 7,698,263,093 aa (total number of residues)
DAD Release Note

Release of TSA data of forest soil metagenome

jmashima — Mon, 18 Mar 2013 04:24:01 +0000

DDBJ released TSA data derived from forest soil metagenome, which had been submitted by National Institute of Advanced Industrial Science and Technology.

The accession numbers are as follows. (Available by getentry and DRASearch)

TSA: FX000001-FX056084 (56,084 entries)
raw data: DRR000345

Changes in the anonymous FTP site: Added a new directory "unified-all" and rename from "non-redundant" to "unified-new"

jmashima — Thu, 07 Mar 2013 07:56:00 +0000

A new directory "unified-all" was added under "ddbj_database" of DDBJ anonymous FTP site. With this addition, a directory, "non-redundant", was renamed to "unified-new"
About the "ddbj_database" directory and its sub-directories, please refer to the README.TXT in the directory. When you monitor the FTP site, please confirm your monitoring program, if necessary.

unified-all; ftp://ftp.ddbj.nig.ac.jp/ddbj_database/ddbjnew/unified-all

This directory contains files of merged sequence entries from all files of ddbj and ddbjnew directories to include only latest version of updated entries (i.e. Succeeded versions of entries have been excluded).

Contents of the directory

　unified-all
　　|- fasta   : in FASTA file format
　　|- blastdb : in BLAST DB format

unified-new; ftp://ftp.ddbj.nig.ac.jp/ddbj_database/ddbjnew/unified-new

This directory contains files of merged cumulative daily updates of sequence entries from all files of ddbjnew directory to include only latest version of updated entries (i.e. Succeeded versions of entries have been excluded) in the flat file format.

Contents of the directory

　unified-new  : in DDBJ flat file format
　　|- fasta   : in FASTA file format
　　|- blastdb : in BLAST DB format