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DDBJ
No.49  Apr. 22, 2010
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 Visiting Mishima - "The Mishima Taisha"
yozakura The Mishima Taisha is a Shinto shrine in the city of Mishima in Shizuoka Prefecture. It is an old and historical shrine. The building is registered as a National Important Cultural Property. The cherry blossoms around here were very beautiful this year, too. The photograph was taken at nignt. The Mishima Taisha is a symbol of Mishima city, a tourist spot and oasis for the citizens.
DDBJ issues DDBJ Mail Magazine (No.49). 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.
 Release of the raw and assembled sequence data set from next-generation sequencers
DDBJ Read Archive (DRA) is an archive for the "raw" output data from next-generation sequencers. DRA stores the un-processed raw data, and DDBJ collects assembled sequence data with annotation. Since 2008, DRA has collected data in cooperative work with NCBI Sequence Read Archive (SRA) and EBI European Read Archive (ERA). see figure.


Here, we report DRA and DDBJ have released 2 data sets of raw and assembled sequence data.

 DRA and DDBJ released genome sequence data of a natto bacterium (Bacillus subtilis subsp. natto str. BEST195), which had been submitted by Sakakibara Laboratory, Keio University. It is the first case that we have accepted and released both raw and assembled sequence data at DRA and DDBJ, respectively.

  DRA accession number: DRA000001
  ⋅DRA000001 data can be downloaded from the Anonymous FTP site.

  DDBJ accession numbers:
  ⋅Genome sequence: AP011541
  ⋅Plasmid pBEST195 sequence: AP011542

 DRA and DDBJ released genome sequence data of Koshihikari rice (Oryza sativa Japonica Group, cultivar Koshihikari), which had been submitted by QTL Genomics Research Center, National Institute of Agrobiological Sciences.

  DRA accession number: DRA000010
  ⋅DRA000010 data can be downloaded from the Anonymous FTP site.

  DDBJ accession numbers:
  ⋅WGS: BABO01000001-BABO01654543 BABO.gz (654,543 entries)
  ⋅scaffold CON: DG000025-DG000036 Oryza_sativa_Japonica_Group_CON_100402_1.seq.gz (12 entries)

  Related announcement: Release of new Koshihikari rice (Oryza sativa Japonica Group, cultivar Koshihikari) WGS 654,543 entries


Currently, DRA has accepted 191 submissions and released 23 submissions. You can see the list of the data released from DRA at Released Data site.
Although we introduce only genome sequence data in this topic, DRA accepts various data for transcriptome analyses, DNA-protein interaction analyses, discoveries of small RNAs, DNA methylation analyses and so on. The next generation sequencers are gaining popularity. It will accelerate the increase ratio of data submission to DRA. DRA makes best efforts to accept submissions more effectively.




April 8, 2010
 Change of UniProt release numbers and release cycle
DDBJ provides the UniProt database (UniProt, UniProt/Swiss-Prot, UniProt/TrEMBL) by anonymous FTP download, and through getentry, ARSA, FASTA/BLAST search services. The data are updated periodically according to the UniProt's updates.
From the issue of March 23, 2010, UniProt changed the release cycle and release numbers. The details are as follows. Please note that the same numbering scheme was applied to Swiss-Prot and TrEMBL release numbers.
          release number format release cycle                            
       current: YYYY_XX 4weeks
       past: x.n 3weeks

where YYYY is the western calendar year and XX is a 2-digit number that is incremented for each release of a given year,
e.g. 2010_01, 2010_02, etc.

Please refer:
 DDBJ Rel. 81 completed

Future DDBJ release schedules
 JPO and KIPO amino acid sequence data are available by anonymous FTP
DDBJ start to distribute amino acid patent data of Japan Patent Office (JPO) and Korean Intellectual Property Office (KIPO), by anonymous FTP from Feb. 26.
For more information, please refer README.TXT about the patent data on anonymous FTP, README.TXT on ddbj_database, and What's New (Feb. 19).
 Release of sequence data from DDBJ (January - March, 2010)
 Release of new tomato (Solanum lycopersicum) GSS 93,682 entries

DDBJ newly released 93,682 entries of GSS data derived from tomato (Solanum lycopersicum), cultivar: Micro-Tom, which had been submitted by University of Tsukuba.
tomato
The accession numbers  (Anonymous FTP)  are as follows ;

These entries were released as DDBJ daily updates on Mar. 3, 2010.
 Release of new mouse (Mus musculus) small RNA MGA 84,606 entries

DDBJ newly released 84,606 entries of small RNAs, MGA data, derived from mouse (Mus musculus), which had been submitted by Kinki University.

mouse The accession numbers are as follows;
  • ANAAA0000001-ANAAA0033164 (33,164 entries)
  • ANAAB0000001-ANAAB0051442 (51,442 entries)
Anonymous FTP: AN_resource_index
Related site: About Mass sequence Genome for Sequence (MGA) entry

These entries were released as DDBJ daily updates on Feb. 16, 2010.
 Release of new pig (Sus scrofa) EST 82,326 entries

DDBJ newly released 82,326 entries of EST data derived from pig (Sus scrofa), which had been submitted by National Institute of Agrobiological Sciences.
buta
The accession numbers  (Anonymous FTP)  are as follows ;

These entries were released as DDBJ daily updates on Feb. 4, 2010.

(Photo: Integrated Database Project)
 Termination of a part of DDBJ services
 DDBJ discontinued services of [FASTA], [SSEARCH], [PSI-BLAST] and [HMMPFAM] provided by WWW and by WebAPI . Click here for more information.

 DDBJ removed "KEGG PATHWAY" from searchable databases in ARSA, as of March 31, 2010.

We apologize for your inconvenience. Thank you for your understanding and cooperation.
  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)
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