DDBJ DNA Data Bank of Japan
No.35    December 27, 2007
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 ♦ Thank you for using DDBJ in 2007 
Time flies. The year 2007 is finishing in 5 days. We DDBJ had a lot of events this year. First, the supercomputer system was replaced after six years. Second, we celebrated the 20th anniversary of starting DDBJ release. Third, we have made a big change on our website. Thank you for using the DDBJ system, and we wish to continue to make use of us next year as well.
If you have any questions and suggestions about DDBJmag, please don't hesitate to write to . We would like to hear from you!!!

 ♦ Revision of DDBJ flat file format: Deletion of E-mail address, phone and fax numbers 
Outline of revision
To follow the Japanese law of protecting personal information, DDBJ will delete both phone and fax numbers, and E-mail address from the flat files of the entries submitted to DDBJ. It would be also helpful to protect the DDBJ releases against SPAM mail senders. DDBJ plans to retorofit the entries submitted to DDBJ, not to GenBank or EMBL, by periodical release 72, the end of December 2007.
Up to now, database users can contact to sequence submitters by using their E-mail addresses on the DDBJ flat files. However, after this revision, it will become difficult to contact submitters. When you wish to contact to the submitter(s) of an entry of your interest, please contact us with the inquiry form (below) with reasons briefly; i.e. asking to transfer cloned sequences, etc, then we will forward your messeage to the submitter(s).
Thank you very much for your understanding and cooperation.
Inquiry Form to Forward Your Question/Request to the Submitter of the DDBJ Entry

Detailed particulars of revision
Now, the submitter information is described in JOURNAL line at REFERENCE 1 as,
  JOURNAL   Submitted (30-NOV-2000) to the DDBJ/EMBL/GenBank databases.
            Hanako Mishima, National Institute of Genetics, DNA Data
            Bank of Japan; Yata 1111, Mishima, Shizuoka 411-8540, Japan
            (E-mail:mishima@supernig.nig.ac.jp, Tel:81-55-981-6853,
After the deletion or the information in question, DDBJ flat file will be either one of the following two types;
Type 1: Phone and fax numbers and E-mail address are deleted.
  JOURNAL   Submitted (30-NOV-2000) to the DDBJ/EMBL/GenBank databases.
            Contact:Hanako Mishima
            National Institute of Genetics, DNA Data Bank of Japan; Yata 1111,
            Mishima, Shizuoka 411-8540, Japan
Type 2: When the submitters wish to keep their contact information disclosed, it will be described as,

  JOURNAL   Submitted (30-NOV-2000) to the DDBJ/EMBL/GenBank databases.
            Contact:Hanako Mishima
            National Institute of Genetics, DNA Data Bank of Japan; Yata 1111,
            Mishima, Shizuoka 411-8540, Japan
            E-mail :mishima@supernig.nig.ac.jp
            Phone  :81-55-981-6853
            Fax    :81-55-981-6849
In principle, we will delete all of the items, "phone number", "fax number", and "E-mail address" from the entries that have been submitted to DDBJ as shown in "Type 1". However, if you wish to disclose any of the three items, please contact us at   , specifying the item(s) to be disclosed.

 ♦ ARSA 2nd Enhancement 
DDBJ fruther upgraded ARSA (All-round Retrieval of Sequence and Annotation) is the high-speed keyword search system provided by DDBJ.

The features of ARSA are as follows:
  • ARSA provides one-stop query to 24 life science databases (30 million entries) including DDBJ International Nucleotide Sequence Database.
  • ARSA will return a quick response to any query regardless of the complexity of the query, the number of hits to the query and the target database(s)
  • In the case of DDBJ, you can define search conditions in details by use of any combination of Features/Qualifiers of the DDBJ flat file.
  • Application Programming Interface (API) is prepared so that you can call some functions of ARSA from your programs such as Java, in your computer.

DDBJ added the following new functions this time.
  • Addition of the KEGG/PATHWAY database to the searchable databases
    KEGG/PATHWAY database was newly added. You can view the PATHWAY maps by clicking the PATHWAY IDs in the result lists.

  • Specification of detailed search conditions in the all databases, as well as DDBJ
    The detailed search conditions can be specified in the all databases (When you use this function, select the database in the top page, then click the "Cross Search" button).

  • Cross Search of multiple databases using the common search conditions
    When you select the multiple databases, you can use the above function by using the common search conditions (Check the multiple databases you would like to search in the top page, then click the "Cross Search" button).
Other improvements:
  • "&(AND)" and/or "|(OR)" can be entered into the search boxes directly
    (e.g. see the "Help" page)
  • The restriction for using the following words in the refine search was removed.
    (In the new ARSA, " ' ", " ( ", " ) ", " { ", " } " can be used as the search keywords)

ARSA New Top Page
Hit Count List Page

ARSA will continue to be enhanced, if you make comments. So, please visit ARSA and click "Your Comment" to help us to improve ARSA to help you.

  ♦ Change of the sequence search system linked with TXSearch 
TXSearch is a retrieval sysytem for a Taxonomy Database unified by EMBL, GenBank and DDBJ. TXSearch is developed by DDBJ.
TXSearch became more useful as the link was switched from SRS to enhanced ARSA in November. When you submit nucleotide sequences, this system could help you not only to retrieve taxonomic names but also to search for the related sequences, organism name or obtaining taxonomic ID from the results.
You will realize the quick retrieval of the related information with this search sysytem.

 ♦ Suspension of the DDBJ activity during the New Year Holidays (2008) 
We at DDBJ will temporally close our business for the New Year Holidays in the following schedules, according to the Japanese custom, and resume the normal business on January 4, 2008. Please note in particular that SAKURA will also stop in operation for a while (see below). However, the computer search and analysis and FTP are available during the holidays.
DDBJ activity suspension: from December 29, 2007 to January 3, 2008
SAKURA suspension: from December 27, 2007 at 17:00 (JST) to January 4, 2008 at 10:00 (JST)
data release suspension: from December 27, 2007 to January 4, 2008

 ♦ The 7th Japan-Korea-China Bioinformatics Training Course (March, 2008) 
We are pleased to announce that "The 7th Japan-Korea-China Bioinformatic Training Course" will be held at the International Center in Jeju University, Korea, in March 18-21, 2008.
This time we will also organize a mini-symposium at which the lectureres of the training course talk about their original research topics. The trainees are expected to attned the mini-symposium, as well.
If you wish to participate in this training course as a trainee, please visit us and check the detail!! (see below website)
The number of Japanese trainees is limited to 10. The trainee is expected to be either a graduate student or a postdoc in bioinformatics who is fluent in English. In addition, the trainee is required to be the passport holder, which is valid more than 6 months at the point of the training course. The deadline of the application is February 8, 2008.
The successful applicant is covered with travel expenses including air and train tickets, lodging and meals. He/She is also provided with a PC linked with Internet during the course.

URL: The 7th Japan-Korea-China Bioinformatics Training Course (March, 2008)
(* Application is starting from 4th January 2008)

 ♦ Apology for releasing of defective files of human gut metagenome WGS data from anonymous FTP 
The thirteen files (BAAU.gz to BABG.gz), which were released from /database/wgs/ or /database2/wgs/ directory of anonymous FTP, had a problem that the each entry was duplicated. The files contain flatfiles for human gut metagenome WGS data.
We deeply apologize for inconveniences. The problem has been resolved now. Please retrieve the corrected files again if you have got defective files during the period until Nov. 12, 2007, 12:30 PM.

  • Period: 2007.10.18 - 2007.11.12 12:30 PM
  • Details of the files:
    Name  Accession numbers
    BAAU.gz   BAAU01000001-BAAU01028900
    BAAV.gz   BAAV01000001-BAAV01036326
    BAAW.gz   BAAW01000001-BAAW01016539
    BAAX.gz   BAAX01000001-BAAX01036455
    BAAY.gz   BAAY01000001-BAAY01030198
    BAAZ.gz   BAAZ01000001-BAAZ01031237
    BABA.gz   BABA01000001-BABA01035177
    BABB.gz   BABB01000001-BABB01020226
    BABC.gz   BABC01000001-BABC01009958
    BABD.gz   BABD01000001-BABD01037296
    BABE.gz   BABE01000001-BABE01020532
    BABF.gz   BABF01000001-BABF01016164
    BABG.gz   BABG01000001-BABG01034797

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
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