HOME > DDBJ Mail Magazine  
No.56 & 57  Mar. 3, 2011
top Latest version top    backnumber backnumber    ddbj Published by DDBJ
 "Suruga kite"
tako This is a photo of "Suruga kite". Suruga kite has unique features; heptagonal form and designs of Kabuki actors or warriors. In Shizuoka, there are a lot of kinds of Japanese kite, Suruga kite, Hamamatsu kite, Enshu Yokosuka kite, Sagara kite, Yaizu fish kite, Igawa fan kite, Nagaizumi kite, Munadaka kite, and so on. Since Edo period, Kite-flying has become familiar among ordinary people as celebration of the birth of boy and one of traditional New Year games. In Japan, a kite soared high in the sky is a good luck charm.
DDBJ issues DDBJ Mail Magazine (No.56 & 57). 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.
 DDBJ Rel. 84.1 and DAD (DDBJ amino acid database) Rel. 54.1 Released
DDBJ released Rel.84.1 and Rel.54.1, because a part of trouble had been found in Rel.84 (released on Dec. 2010) and Rel.54 (released on Jan. 2011).

Reference: Apologies for the trouble of in DDBJ release 84, Apologies for the trouble of in DAD release 54
 DDBJ/EMBL/GenBank Feature Table Definition revised
Feature Table Definition(FT-Doc) is the common annotation manual among the three banks(DDBJ, EMBL-Bank, GenBank) for the construction of the DDBJ/EMBL/GenBank International Nucleotide Sequence Database. Following the decision at an International Collaborators Meeting(ICM) held annually in May, this FT-Doc is updated every year. In January 2011, FT-Doc is updated, based on the 23rd International Collaborators Meeting.
 Report for DDBJ activities in NAR
DDBJ activities were introduced in the following papers appeared in Nucleic Acids Research Vol.39 Database Issue (Jan.2011).

"The International Nucleotide Sequence Database Collaboration"
Guy Cochrane, Ilene Karsch-Mizrachi, and Yasukazu Nakamura on behalf of the International Nucleotide Sequence Database Collaboration.
Nucleic Acids Research, 2011, Vol. 39, Database issue D15-D18

"The Sequence Read Archive"
Rasko Leinonen, Hideaki Sugawara, and Martin Shumway on behalf of the International Nucleotide Sequence Database Collaboration.
Nucleic Acids Research, 2011, Vol. 39, Database issue D19-D21

"DDBJ progress report"
Eli Kaminuma, Takehide Kosuge, Yuichi Kodama, Hideo Aono, Jun Mashima, Takashi Gojobori, Hideaki Sugawara, Osamu Ogasawara, Toshihisa Takagi, Kousaku Okubo, and Yasukazu Nakamura.
Nucleic Acids Research, 2011, Vol. 39, Database issue D22-D27
 DDBJ will continue Sequence Raw Data Archiving

DDBJ has been archiving raw data from Sanger sequencers and so called next-generation sequencers as a part of EBI/NCBI/DDBJ International Nucleotide Sequence Database Collaboration (INSDC), by receiving data submissions from sequence centers mainly in Japan and also from several other countries.

The data submitted to DDBJ are processed into INSDC approved format and exchanged among NCBI and EBI frequently to make a same data set in either bank at the timing of data publication to minimize the difference in convenience of data access from all over the world.

In light of the recent announcement that NCBI, who has been playing a hub in raw data archiving, will discontinue its Sequence Read Archive and Trace Archive repositories, DDBJ's archiving will be affected somehow in the near future.

However, at this moment, DDBJ does not plan to discontinue either of the service to meet the demand of the domestic community as well as of the global one.

DDBJ has just started to formulate the plan to minimize the effect to the present activity of INSDC as well as the entire community in collaboration with other INSDC members.

  Reference: DDBJ will continue Sequence Raw Data Archiving
 DRA directory composition of FTP was changed
"dra" directory composition of DDBJ FTP site was changed.
The data which had been placed under /ddbj_database/dra are available in "fastq", and SRA lite formatted data are newly available in "sralite". SRA lite contains sequence and fastq data.
For details, please see README.TXT. If you automatically monitor DDBJ anonymous FTP, please confirm your monitoring program if necessary.
 Release of sequence data from DDBJ (Dec. 2010 - Feb. 2011)
DDBJ newly released GSS data derived from rice (Oryza sativa Japonica Group ), which had been submitted by National Institute of Agrobiological Sciences.

The accession numbers are as follows ;
  • FT872362-FT932077 (59,716 entries)

These entries were released as DDBJ daily updates on Feb. 25, 2011.

DDBJ newly released 131,507 entries of GSS data derived from mouse (Mus musculus domesticus ), which had been submitted by RIKEN BioResource Center.

The accession numbers (Anonymous FTP) are as follows ;

DDBJ released genome sequence of an uncultivated thermophilic archaeon (Candidatus Caldiarchaeum subterraneum), which had been submitted by the Japan Agency for Marine-Earth Science and Technology.

The accession numbers (file name for Anonymous FTP download) are as follows ;

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

·AB201309 ·AP011633
·AP011826 - AP011902
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