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DDBJ
No.54 & 55  Dec. 20, 2010
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 "Satsuma mandarin"
Satsuma mandarin Shizuoka is well known as a production center for the satsuma mandarin (Citrus unshiu). It is harvest time now. Satsuma mandarin is indispensable for New Year's Holidays in Japan. The family in Japan encloses the kotatsu, and eats the satsuma mandarin while watching television. Kotatsu is a low table with an electric heater attached to the underside. However, such a spectacle in a New Year might be decreasing recently.
DDBJ issues DDBJ Mail Magazine (No.54 & 55). 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.
 Suspension of the DDBJ activity during the New Year Holidays
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 4th, 2011.
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 Dec. 29(Wed), 2010 to Jan. 3(Mon), 2011
       SAKURA suspension: from Dec. 27(Mon), 2010 at 17:00 to Jan. 4(Tue), 2011 at 10:00(JST)
       data release suspension: from Dec. 27(Mon), 2010 to Jan. 4(Tue), 2011
Thank you very much for your understanding and cooperation. We wish you a Happy New Year.
 DDBJ will terminate accepting submission by 'Sequin'
DDBJ has accepted nucleotide sequence data submissions by SAKURA, MSS(Mass Submission System), or 'Sequin'. However, DDBJ will terminate accepting submission by 'Sequin' as of the end of January, 2011. Alternatively, by using SAKURA or MSS, you can submit your data easily and quickly by far. Please use SAKURA or MSS hereafter.
Please use SAKURA or Mass Submission System (MSS) for your future submission to DDBJ.

Reference: Workflow of the data submission to DDBJ
(A) SAKURA
(B) Mass Submission System (MSS)

If you need 'Sequin' submission by unavoidable reason, please send your data to GenBank.
Reference: http://www.ncbi.nlm.nih.gov/Sequin/

Thank you for your cooperation and understanding.
 First Japanese whole genome sequencing data are released from the DDBJ Sequence Read Archive
Center for Genomic Medicine, RIKEN analyzed the whole genome sequence of a Japanese male which had been genotyped by the International HapMap project. As a result, the research group identified over 3 million single nucleotide variations (SNVs), 5,319 deletions smaller than 10 kb as well as 3 million base pairs of novel genome sequences were not found in the human reference genome (Press release from RIKEN).

DDBJ Sequence Read Archive has released the sequencing data of the Illumina Genome Analyzer II used in this analysis under the accession number DRA000222.
 DDBJ Sequence Read Archive has released the data search system
DDBJ Sequence Read Archive has released the data search system (beta). You can search all public data of the DDBJ/EBI/NCBI Sequence Read Archive by accession number, organism name, submitting center name, sequencing platform and study type. Keyword search will be implemented. Metadata is available in XML file and sequencing data can be downloaded in fastq file format. Please try our search system and send us your feedback. For data search of DDBJ/EMBL-Bank/GenBank entries, please use getentry and ARSA.

DDBJ Sequence Read Archive is a public repository for next-generation sequencing data at primary analysis phase.
 BLAST Web API against RefSeq database was opened to the public from WABI
Following databases of RefSeq has been added to High Speed BLAST API in addition to DDBJ.
Furthermore, Reference proteins (sample program) has been added as a reference database of usual BLAST API.
Use case and execution time
It is possible to do a fast BLAST search against RefSeq databases as well as DDBJ. For example, the following case can be calculated only in a minute. It may change according to whether our server accepts a lot of jobs or not.

Case 1. Comparison between full length cDNA of human and multiple genomes.
Sample program can be available here.

Condition:
  • Program: blastn
  • Reference database: Reference genomic sequences (2 million sequences, Total 140 billion bases)
  • Query: Full length cDNA of human gene ALDH2 (DDBJ Accession: BC002967, Sequence length: 2050 bp)
  • Parameter: -b 100 -v 100

Result:
Human and a list of homologous species such as horse, dog, chimpanzee, orangutan and rhesus monkey can be obtained. Furthermore, chromosome number and the position on it of their genome or whole genome shotgun can also be obtained.
Case 2. Comparison between environmental DNA sequence and multiple genome.
Sample program can be available here.

Condition:
  • Program: blastn
  • Reference database: Reference genomic sequences (2 million sequences, Total 140 billion bases)
  • Query: Environmental DNA sequence (DDBJ Accession: HQ188503, Sequence length: 508 bp)
  • Parameter: -b 100 -v 100 -W 28 -X 20 (equivalent to megablast)

Result:
A list of the psychrophilic bacterial species of Shewanella genus can be obtained. Furthermore, the homologous region of their genomes can be also obtained. It is verified that those regions are 16S ribosomal RNA by checking annotations of genomes.
Please refer to the page for details.
 Organism information on SAKURA was changed
SAKURA is a nucleotide sequence data submission system through the WWW server at DDBJ.
"Organism Information" page has been improved. The input method of organism name has changed on SAKURA from Oct. 26, 2010. Details about the actual input method, please see SAKURA's organism information page which is shown after you start the submission, SAKURA's help page, and Sequence data submission via SAKURA.
  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
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