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DDBJ
No.51  Aug. 31, 2010
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 "Mt. Fuji of summer"
natunofuji The snowcapped Mt. Fuji is famous but its color is blue in summer. Of course, there is permafrost on the top of a mountain. The best season to climb Mt. Fuji is from July to August. However, the temperature at the top of the mountain is chilly 5.6℃ in the midsummer. The row of lights of people climbing Mt. Fuji can be seen from town at the foot of the mountain at night if the sky is clear. The sight of Mt. Fuji from a distance is nice. If you climbed on the top of Mt. Fuji, you could encounter stunning vista.


DDBJ issues DDBJ Mail Magazine (No.51). 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.
 "Patent" was added to the BLAST protein search
DDBJ added patent data to the protein data base of BLAST on August 24, 2010. Japan Patent Office (JPO), Korean Intellectual Property Office (KIPO), United States Patent and Trademark office (USPTO) and European Patent Office (EPO) can be selected. The update is scheduled about four times a year.

patent
 The NCBI RefSeq data was released in the mirror
DDBJ has started to mirror the NCBI RefSeq data from August 23, 2010. You can download the RefSeq data from DDBJ's Anonymous-FTP site (ftp://ftp.ddbj.nig.ac.jp/mirror_database/refseq/release/).
The directory hierarchy under "/release" is the same as that of NCBI.. The update is scheduled about twice times a month.
 DRA has started to distribute public data of DRA/ERA/SRA
DRA collects and distributes raw output data from next-generation sequencers with NCBI Sequence Read Archive and EBI Sequence Read Archive.
You can download the metadata XML and fastq files released from DRA/ERA/SRA at DRA Download (FASTQ) site.

And, DDBJ/EBI/NCBI has decided to call this international activity as "Sequence Read Archive". According to this, we have changed our database name from "DDBJ Read Archive" to "DDBJ Sequence Read Archive".
 DDBJ Rel. 82 and DAD Rel. 52 Completed

Future DDBJ and DAD release schedule
DDBJ will make up its periodical DDBJ Rel. 83 and DAD Rel. 53 in September 2010 as usual. Though we had informed "DDBJ periodical release 83 and release 53 would be prepared in December 2010" in the previous release note, we reconsidered to take back the schedule of DDBJ periodical releases. We apologize for the confusion.
 Termination of DDBJ-XML output format
DDBJ-XML is one of the data output formats, which DDBJ designed based on XML. DDBJ discontinued providing DDBJ-XML data on Jun. 25, 2010. The details are as follows. We apologize for your inconvenience. Thank you for your understanding and cooperation.

 Termination schedule: Jun. 25, 2010
Services Termination
DDBJ periodical release
DDBJ new data
DDBJ-XML format of Anonymous-FTP
getentry DDBJ-XML format of retrieval result of web, E-mail and FTP data
WABI getXML_DDBJEntry of GetEntry
getXMLEntry of DDBJ

 The conversion tool is provided. The details are as follows:

 Release of sequence data from DDBJ (June - July, 2010)
 Release of new fission yeast GSS 113,551 entries and EST 101,079 entries
DDBJ newly released GSS: 113,551 entries and EST: 101,079 entries derived from fission yeast (Schizosaccharomyces pombe ), which had been submitted by Osaka City University.

koubo
The accession numbers are as follows ;

These entries were released as DDBJ daily updates on Jul. 28, 2010.
(Photo: Integrated Database Project)
 Release of new mouse (Mus musculus ) embryo small RNAs, MGA 397,593 entries

DDBJ newly released small RNA sequences, 397,593 entries of MGA data derived from mouse (Mus musculus) embryos, which had been submitted by National Institute of Neuroscience.

The accession numbers  (Anonymous FTP)  are as follows ;
  • ALAAA0000001-ALAAA0130942 (130,942 entries)
  • ALAAB0000001-ALAAB0116883 (116,883 entries)
  • ALAAC0000001-ALAAC0092019 (92,019 entries)
  • ALAAD0000001-ALAAD0057749 (57,749 entries)
Anonymous FTP: AL_resource_index.html

These entries were released as DDBJ daily updates on Jun. 15, 2010.
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