DNA Data Bank of Japan
DDBJ Mail Magazine 
December.19, 2005
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Copyright © 1995-2006
DDBJ All rights reserved.
 ♦Notice for DDBJing in Osaka 
DDBJing is a series of lectures about DDBJ services. DDBJ has irregularly hold DDBJing in many parts of Japan so that users can make the best use of database search and analysis at DDBJ. In DDBJing, our staffs generousely give lectures for deeper understanding of DDBJ services and for concrete exercise of search and analysis tools.
On February 2nd and 3rd, 2006, we are going to hold [14th DDBJing & 2nd PDBjing] in Osaka.
Same as the last [DDBJing and PDBjing], it is jointly hosted by DDBJ and PDBj (Protein Data Bank Japan) so that you can learn about not only DDBJ services but also the services provided by PDBj of how to use the database of amino acid and protein. In these courses, we are planned to spare more time to computer basis training in order to aquire much practical knowledge for users' convenience. We are looking forward to seeing you at DDBJing in Osaka.
We started accepting application for DDBJing from December 5, 2005. If you have interests and live near this location, please click "For datails" for more information. We are sorry for your inconvenience that in this time, DDBJing give lectures only in Japanese.
For datails (Japanese only)
  • Date: February 2nd, 2006 (Thr) 13:00 to February 3rd, 2006 (Fri) 17:00
  • Location: Osaka University at Nakanoshima Center Campus Innovation center
  • Target: Anyone who make use of DDBJ and PDBj
  • Mandatory: Since we use Network with wireless LAN, you are expected to bring your PC with the function of wireless LAN adpter.
 ♦ INSD-XML formatted periodical release data available at FTP. 
The nucleotide sequence database collected and maintained by DDBJ is quarterly released to the public at online anonymous FTP site. DDBJ has provided 4 types (Flat file format, FASTA format, DDBJ-XML format and CDS sequences) data so far.
Additionally, since DDBJ Release62 (June 2005) the INSD-XML formatted periodical release data also have been provided by DDBJ. The INSD-XML formatted data had been available only daily update part since April 29, 2005.
The INSD-XML is one of the DTD (Data Type Definition) commonly used by the International Nucleotide Sequence Database Collaboration (INSDC) which is comprised of DDBJ, EMBL, and GenBank, for their data releases. Although the INSD-XML was released to the public, the INSDC will confirm that there are no problems in the data exchange for all entries, and also will ensure that it is possible to write/read XML documents in a common format. Therefore, in some cases, DTD itself might be changed and/or some changes might be made at the stage of the development from DTD to XML document. The version number is shown in the DTD file.
The anonymous FTP directories and the file names released at DDBJ web pages are as shown below.
  • Use of the INSD-XML at FTP
    URL: ftp://ftp.ddbj.nig.ac.jp/ddbj_database/ddbj/xml/insd/
  • DTD for the INSD-XML (INSD_INSDSeq.dtd) is located in the same directory.
  • Use of the INSD-XML at getentry
    If you specify "INSD-XML" as output format in DNA database retrieval, you will obtain the data in the INSD-XML format.
  • The difference between DDBJ-XML and INSD-XML
    DDBJ-XML was designed aiming for the generation of documents making easier computer program manipulation and being also readable by humans. It is based on the concept of "flat file format", which has been widely used so far.
    Meanwhile, INSD-XML was designed focusing on Features/qualifiers structure rather than having familiarity with the Flat File format.
Reference
Release of INSD-XML formatted data (Jun. 10, 2005)
The DDBJ release is now available also in XML (Jul. 25, 2001)
DDBJ introduced XML (May 11, 2001)

 ♦ A new "Graphical View" function was added to the web BLAST search program 
clustalw Graphical View image BLAST search services are provided by DDBJ via the web and e-mail server. Since November 1, a new "Graphical View" (optional) function was incorporated to the web version of the BLAST search program.
As default setting the check box of the "Graphical View" is selected to display the results of the homology search. The top bar in blue represents the query sequence whose length is shown by a scale. Colored arrows indicate regions and directions of sequences matched to the query sequence. By clicking these arrows, you can jump to the respective alignments. Furthermore, you can easily transfer sequences to CLUSTALW analysis by checking the boxes on the left side of each arrow, and then click "CLUSTALW SETUP". Alternatively, if you do not use the "Graphical View" option, select sequences for "CLUSTALW" test by using the "Select Sequences" menu of the result page.

 ♦ Suspension of the DDBJ activity during the New Year Holidays 
We DDBJ will suspend our business for receiving and releasing data during the New Year Holidays from December 29th, 2005 to January 3rd, 2006.
We will resume the normal business on January 4th, 2006.
Please note in particular that SAKURA will stop in operation from December 27th, 2005 to January 4th, 2006 and the new daily update will not be released in the period from December 27th, 2005 to January 4th, 2006.
Thank you very much for your understanding and cooperation.
We extend our very best wishes for a happy Holiday Season.
    DDBJ activity suspension from December 29th, 2005 to January 3rd
    SAKURA suspension from December 27th, 2005 to January 4th
    data release suspension from December 27th, 2005 to January 4th


 ♦ Incomplete release of WGS data at FTP 
DDBJ releases WGS data at anonymous ftp site.
WGS data were not released from September 8th to November 10th at DDBJ ftp site. We had already added the un-released data, and now all WGS data are available.
We sincerely apologize for this.
List of released files

 ♦28th Annual Meeting of the Molecular Biology Society of Japan 
DDBJ presented a poster titled "Overview of DDBJ activities: Contribution to the research of information biology" at 28th Annual Meeting of the Molcular Biology Society of Japan in Fukuoka from December 7 to 10, 2005.
Our activities and services were introduced, including "SAKURA" sequence submission system, "getentry" sequence retrieval system, INSDC: International Nucleotide Sequence Database Collaboration, "ARSA: All-round Retrieval of Sequence and Annotation", and MGA data (Mass sequence for Genome Annotation).

 ♦ For any questions... 
If you have any questions and opinions about DDBJmag, please don't hesitate to write to ddbjmag@ddbj.nig.ac.jp. We really want to hear from you!!!!



Published by: DNA Data Bank of Japan (DDBJ)
  Center for Information Biology and DNA Data Bank of Japan (CIB-DDBJ)
National Institute of Genetics (NIG)
Research Organization of Information and Systems
1111 Yata, Mishima, Shizuoka 411-8540, JAPAN
Last modified: Oct. 07, 2011