DNA Data Bank of Japan
DDBJ Mail Magazine 
November 12, 2007
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 ♦We have serial excietments 
We found a hornet's nest outside our office window. We were watching through the window being safe inside. We had never seen how they constructed the nest and were excited by watching it growing and changing everyday. However, it ended, because hornets came into our office now, and then we had to ask for its removal. They lost the nest and they trid to find their home in vain. It makes us very sad. We could have enjoyed if the hornets had never been harmful.
If you have any questions and suggestions about DDBJmag, please don't hesitate to write to . We really want to hear from you!!!
office window hornet's nest
4th floorartisitic shape

 ♦DDBJ HP Renewal! 
We updated our home page this October to make our data submitters and users comfortable at the DDBJ site.

The key points of the updating are as follows:
  • Redesign of our site navigation system
    Based on a current trend of web site design,
    • we have placed a global menu near the top of the page, and
    • local (context-sensitive) menus at the left- hand side of each page. Furthermore,
    • the bread-crumb trail is located under the left corner of the global menu to help you avoid losing your way in our web site.
    In the new HP when you click one of the global menus, you can observe all the contents of each service at a glance, and make the best choice without stress.

  • Creation of a window for searching databases at the top of each page
    In the new HP, you can search following types of data from the search window, without migrating to the main page of the databases here and there.
i) accession numbers (by getentry)
ii) keywords in DDBJ release and daily update (by SRS)
iii) keywords in Protein databases (by SRS)
iv) Scientific names and names of taxa (by TXSearch)
v) Full text search in the DDBJ site

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

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

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

Kurokawa,K et al. (2007). DNA Res. 18:1-13

The accession numbers are as follows;

BAAU01000001-BAAU01028900 (28900 entries) (BAAU.gz)
BAAV01000001-BAAV01036326 (36326 entries) (BAAV.gz)
BAAW01000001-BAAW01016539 (16539 entries) (BAAW.gz)
BAAX01000001-BAAX01036455 (36455 entries) (BAAX.gz)
BAAY01000001-BAAY01030198 (30198 entries) (BAAY.gz)
BAAZ01000001-BAAZ01031237 (31237 entries) (BAAZ.gz)
BABA01000001-BABA01035177 (35177 entries) (BABA.gz)
BABB01000001-BABB01020226 (20226 entries) (BABB.gz)
BABC01000001-BABC01009958 ( 9958 entries) (BABC.gz)
BABD01000001-BABD01037296 (37296 entries) (BABD.gz)
BABE01000001-BABE01020532 (20532 entries) (BABE.gz)
BABF01000001-BABF01016164 (16164 entries) (BABF.gz)
BABG01000001-BABG01034797 (34797 entries) (BABG.gz)

These entries were released as DDBJ daily updates on Nobember 12, 2007, and are available by anonymous FTP

Related Links:

 ♦DDBJ Rel. 71 Completed 
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public. We completed DDBJ Release 71 in September 27, 2007. DDBJ Release 71 consists of 76,273,34 entries, and the number of bases reached 79,706,204,461. FTP site for periodical release and new data download As was already notified at DDBJ HP, DDBJ will delete both phone and fax numbers, and E-mail address from the flat files of the entries submitted to DDBJ. DDBJ plans to retorofit the entries submitted to DDBJ, not to GenBank or EMBL, by periodical release 72, the end of December 2007. For the details of this DDBJ flat file format revision, please see here.  

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

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

  2. REST is easy to treat large-scale data.
    REST service provides you with the result as a stream. Therefore you can retrieve the result line by line, and this lowers the machine load since the retrieved result isn't saved to the computer memory. So you can retrieve large-scale data effectively by using REST service compared to SOAP. For example, if you want to retrieve DDBJ genome data of Escherichia coli with flat file format, REST service provides you with more than three times speed compared to SOAP.
On the other hand, SOAP service has also advantages that coding volume is small and it has extensibility.

DDBJ will enhance WEB API (Application Program Interface) in the future to be more easy to use. Please contact xml-admin@ddbj.nig.ac.jp, if you have any opinions or suggestions.

* What is REST?

 ♦The distribution of massive entries  
The massive sequence data which were collected by DDBJ and released through the INSD (International Nucleotide Sequence Database) from this August to September are as follows:

Release of Silkworm GSS 94,904 entries Sep. 20, 2007 DDBJ released silkworm (Bombyx mori) GSS 94,904 entries, which had been submitted by National Institute of Agrobiological Sciences. These entries were released as DDBJ daily update on 9/14. Reference URL: http://sgp.dna.affrc.go.jp/ The accession numbers and the file names for anonymous FTP are as follows;

Release of Cycas taitungensis mitochondrion WGS data Sep. 20, 2007 DDBJ released Cycas taitungensis mitochondrion WGS data which had been been submitted by Academia Sinica, Research center for Biodiversity. The accession numbers and the file names for anonymous FTP are as follows;

Published by: DNA Data Bank of Japan (DDBJ)
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Last modified: Oct. 07, 2011