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DDBJ
No.52 & 53  Oct. 26, 2010
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 "Wasabi"
wasabi-1 The view of the photo is wasabi field in Nakaizu. Nakaizu is one of the most famous wasabi growing areas in Japan. Wasabi is grown in pure cold water and equable climate. It is difficult to cultivate. It is an essential spice for cold soba noodles, sushi and sashimi. Please come to see the beautiful wasabi field. And please taste a delicious wasabi.
DDBJ issues DDBJ Mail Magazine (No.52 & 53). If you have any questions and suggestions about DDBJmag, please do not hesitate to write ddbjmag@ddbj.nig.ac.jp . We would like to hear from you.
 Trace data determined by "Human full-length cDNA sequencing projects" are available
A total of 2,445,650 traces determined by the New Energy and Industrial Technology Development Organization (NEDO) "Human full-length cDNA sequencing projects" used to construct the human full-length cDNA clones are available.
These data are available at *DDBJ Trace Archive and NCBI Trace Archive.

  TI numbers:
    ∙ 2282248605-2282527996
    ∙ 2282791904-2284232295
    ∙ 2284242226-2284960269
    ∙ 2284238627-2284240689
    ∙ 2285528775-2285534533

  Anonymous FTP:
    ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dta/FLJ/

*: DDBJ Trace Archive (DTA) is a permanent repository of DNA sequence chromatograms (traces), base calls, and quality estimates for single-pass reads from various large-scale sequencing projects.
 SAKURA specification changed
SAKURA is a nucleotide sequence data submission system through the WWW server at DDBJ. SAKURA has been open to public and continuously refined since 1995.

On October 26, 2010, DDBJ executed the specification changes around input items for "Organism Information" page, and some related changes. Details are as follows:
1. Improvement of "Organism Information"input page.
   Please refer to the SAKURA's help page for a new input method.
2. Clean up of old templates.
   a). removed all saved templates
   Currently, you cannot use your previous templates.

   b). The period of template retention was changed to 6 months
   After 6 months from making, your template is automatically removed from SAKURA server.


Thank you for your understanding and cooperation.
 The Report for the 23rd International Collaborators Meeting
International Nucleotide Sequence Database Collaboration (INSDC), consisted of DDBJ, EBI and NCBI, hold the international collaborators meeting every year.

In 2010, the meeting was held at EBI in UK, 19-21 May, to discuss practical matters to maintain and update nucleotide sequence data archives; DDBJ, EMBL-Bank, GenBank, Sequence Read Archive and Trace Archive. As a result of travel disruptions relating to the Icelandic volcano, the meeting was shorter than expected. Despite these difficulties, we believe that we made significant progress at the meeting. The outcomes of the meeting are summarized http://www.ddbj.nig.ac.jp/insdc/icm2010-e.html.
 DDBJ Rel. 83 and DAD Rel. 53 Completed

 - Latest Release Information
 - DDBJ∙DAD Release/daily-update FASTA format change
 - Apologies for the trouble of FASTA file in DAD release
 - According to the Agreement of the 23rd International Collaborative Meeting, held in this May, The DDBJ/EMBL/GenBank Feature Table: Definition will be revised by the next release issue.
 DDBJ ∙ DAD Release/daily-update FASTA format change
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public as the "DDBJ/DAD periodical releases". Moreover, updated data after the cutoff date of the periodical release are released as "ddbjnew/dadnew" every day.
The FASTA format for the DDBJ/DAD periodical and daily update is changed. The details are as follows:

Changed Data (These are available at anonymous FTP)

Data Type Change Coverage
ddbjnew/fasta Upper-case letters → Lower-case letters DDBJ Rel.83 and
DDBJNEW issued after DDBJ Rel.83 cutoff date
ddbjnew/cdsdb Removal of "//" from the end of the entry
dadnew/fasta

Change in the Services

Database Change Coverage
getentry
DNA database
CDS amino acid seq FASTA Removal of "//" from the end of the entry DDBJ Rel.83 and
DDBJNEW issued after DDBJ Rel.83 cutoff date
CDS nt seq FASTA
PROTEIN database
amino acid seq FASTA Removal of "//" from the end of the entry DDBJ Rel.83 and
DDBJNEW issued after DDBJ Rel.83 cutoff date
nt seq FASTA (for DAD)
 
supernig
ddbj, ddbjnew/fasta Upper-case letters → Lower-case letters DDBJ periodical release
dad/fasta Removal of "//" from the end of the entry DAD periodical release
September 15, 2010
 Apologies for the trouble of FASTA file in DAD release
In DAD release (DDBJ amino acid database), FASTA file had a part of trouble during the following period. Details are as follows:

Corresponding releases: DAD release 10, 18 to 52
Situation:
 - An amino residue length over the following size was not correctly displayed in the FASTA format.
    DAD release 10: 7,000 residues or more.
    DAD release 18 to 52: 30,000 residues or more.
 - When an amino residue length was over the above size, correct number was not output to the comment line.
    mistake: CP000108-608|ABB27887.1|30030|Chlorobium
    right: CP000108-608|ABB27887.1|36805|Chlorobium
Services: Anonymous FTP(DAD), supernig
Measure: Correct data was released in DAD release 53

We apologize for your inconvenience.
 Release of sequence data from DDBJ (Sep. - Oct. 2010)
 Release of new kale (Brassica oleracea var. acephala ) EST 119,204 entries
DDBJ newly released 119,204 entries of EST data derived from kale (Brassica oleracea var. acephala ) , which had been submitted by Kirin Holdings Company, Ltd.

The accession numbers  (Anonymous FTP)  are as follows ;

These entries were released as DDBJ daily updates on October 13, 2010.
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Trace data determined by "Human full-length cDNA sequencing projects" are available
SAKURA specification changed
The Report for the 23rd International Collaborators Meeting
DDBJ Rel. 83 and DAD Rel. 53 Completed
DDBJ ∙ DAD Release/daily-update FASTA format change
Apologies for the trouble of FASTA file in DAD release
Release of sequence data from DDBJ (Sep. - Oct. 2010)

      

      

Thank you very much.

  ddbjmag@ddbj.nig.ac.jp
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