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DDBJ Mail Magazine
No.42 & 43   May 29, 2009
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  From Pink to Green
greenNIG In the April, our Institute was fully covered with pink cherry blossoms. And now in May, it completely changed to fresh green leaves. Invigorating scent of young green leaves comes to the office rooms when we open the window.
This is the DDBJ Mail Magazine, double number of 42 & 43.
If you have any questions and suggestions about DDBJmag, please do not hesitate to write to ddbjmag@ddbj.nig.ac.jp . We would like to hear from you.

 Release of Swine Influenza A (H1N1) Virus by DDBJ/EMBL/GenBank Database
Release of Swine Influenza A (H1N1) Virus by DDBJ/EMBL/GenBank International Nucleotide Sequence Database.

The accession numbers (Anonymous FTP) are as follows;(These entries are also available by getentry or ARSA)(As of April 30, 2009)
  • FJ966079-FJ966086
  • FJ966952-FJ966983   (Influenza_A_virus.ff.gz)
Reference URLs:
Phylogenetic tree of HA (hemagglutinin) obtained form recent recent human cases of swine influenza A virus (H1N1) infections.
Click here.
 New release and update of human and mouse MGA data used for a gene network analysis
The international FANTOM consortium, led by the Institute of Physical and Chemical Research of Japan (RIKEN), identified a large-scale gene network which controlled differentiation of the human myeloid leukemia cell line THP-1 from monoblast to monocyte by applying the next-generation sequencing technology and CAGE (Cap Analysis of Gene Expression) method, which RIKEN Omics Science Center (OSC) had developed. In addition, the FANTOM consortium made new discoveries, including uncovering a novel class of non-coding RNA (ncRNA), newly termed tiRNA.

The accomplishments have been made possible through the activities of FANTOM 4, following the preceding FANTOM 1-3, the fourth stage of the FANTOM consortium which has been taking the initiative in the analysis of the mammalian transcriptome. The articles have been published online in "Nature Genetics" and "Genome Biology" since April 19th (April 20th [JST]).

Approximately 30,000,000 MGA (Mass sequence for genome annotation) entries which are related to the research have already been registered in DDBJ and released to the public from The International Nucleotide Sequence Databases. All of the data can be retrieved and viewed with the DDBJ retrieval tool, getentry.

References:

The accession numbers for the MGA entries are as follows:

New Releases

Total: 10,849,945 entries

Updates

Total: 19,073,068 entries



These entries were released as DDBJ daily updates on April 17th, 2009, and are available by getentry or by anonymous FTP.
 Release of sequence data from DDBJ
Release of new Japanese common newt (Cynops pyrrhogaster) EST 25,600 entries May 1, 2009

DDBJ newly released 25,600 entries of EST data derived from Japanese common newt (Cynops pyrrhogaster), which had been submitted by Kyoto University. nihon_imori
The accession numbers are as follows;
  • FS290155-FS315754 (25,600 entries)

These entries were released as DDBJ daily updates on April 25, 2009, and available by getentry or ARSA.

(Photo:provided by the submitter)


Release of new chinese licorice (Glycyrrhiza uralensis) EST 50,594 entries Apr. 24, 2009
DDBJ newly released 50,594 entries of EST data derived from rhizomes of chinese licorice (Glycyrrhiza uralensis), which had been submitted by Chiba University.

The accession numbers  (Anonymous FTP)  are as follows;
These entries were released as DDBJ daily updates on April 24, 2009.


Release of rat GSS 227,486 entries Apr. 1, 2009 DDBJ newly released rat (Rattus norvegicus LE/Stm) GSS 227,486 entries, which had been submitted by Kyoto University.

Reference URL:
    http://www.anim.med.kyoto-u.ac.jp
The accession numbers (Anonymous FTP)  are as follows;

These entries were released as DDBJ daily updates on April 1, 2009.


Release of new tomato full length cDNA (HTC) data 10,959 entries and EST data 27,216 entries Mar. 19, 2009
DDBJ newly released sequence data, tomato (Solanum lycopersicum) full length cDNA (HTC) 10,959 entries and EST 27,216 entries, which had been submitted by Kazusa DNA Research Institute.

Reference URL:
    http://www.pgb.kazusa.or.jp/kaftom/
    http://www.kazusa.or.jp/jsol/microtom/indexe.html

The accession numbers (Anonymous FTP)  are as follows;

These entries were released as DDBJ daily updates on 3/19.


Release of new human CAGE MGA 7,824,360 entriesMar. 1, 2009 DDBJ newly released MGA 7,824,360 entries derived from human acute monocytic leukemia cell line (THP-1) CAGE, which had been submitted by RIKEN.

Reference URL: http://www.osc.riken.jp/
The accession numbers are as follows;
  • AFAAA0000001-AFAAA0543260 (543,260 entries)
  • AFAAB0000001-AFAAB0191814 (191,814 entries)
  • AFAAC0000001-AFAAC0474745 (474,745 entries)
  • AFAAD0000001-AFAAD0353461 (353,461 entries)
  • AFAAE0000001-AFAAE0270208 (270,208 entries)
  • AFAAF0000001-AFAAF0513982 (513,982 entries)
  • AFAAG0000001-AFAAG0349448 (349,448 entries)
  • AFAAH0000001-AFAAH0425524 (425,524 entries)
  • AFAAI0000001-AFAAI0358861 (358,861 entries)
  • AFAAJ0000001-AFAAJ0285303 (285,303 entries)
  • AFAAK0000001-AFAAK0327328 (327,328 entries)
  • AFAAL0000001-AFAAL0456381 (456,381 entries)
  • AFAAM0000001-AFAAM0436519 (436,519 entries)
  • AFAAN0000001-AFAAN0499442 (499,442 entries)
  • AFAAO0000001-AFAAO0682996 (682,996 entries)
  • AFAAP0000001-AFAAP0716451 (716,451 entries)
  • AFAAQ0000001-AFAAQ0546880 (546,880 entries)
  • AFAAR0000001-AFAAR0391757 (391,757 entries)
Related site: About Mass sequence Genome for Sequence (MGA) entry
Anonymous FTP AF_resource_index: ftp://ftp.ddbj.nig.ac.jp/ddbj_database/mga/AF_resource_index.html

These entries were released as DDBJ daily updates on February 27, 2009.

 Update: a database of re-annotated microbial genomes
GTPS (Gene Trek Prokaryote Space) is a re-annotated database which includes public prokaryotic genome sequences and those annotation. Especially, candidates of ORFs are validated and ranked based on a stable and consistent protocol. GTPS has been updated every year. The latest GTPS which includes 690 strains was opened to the public on Mar. 25, 2009. This time, a common menu was installed in top page, genome viewer and feature viewer in addition to the updating of database. Furthermore, the page which explains the procedure of analysis was also opened to the public.
Renewal GTP top page
"common menu" is newly added (red squqre)
Flow chart of analysis procedure of GTPS
 8th Japan-Korea-China Bioinformatics Training Course was held in Kyoto
"The 8th Japan-Korea-China Bioinformatic Training Course" was held at the Kyoto University, Kyoto, Japan, in February 25-28, 2009.
This JKC Training Course is held annually, targeting for the Asian young researchers of this 3 countries, for the purpose of providing the opportunity to promote mutual communication, as well as to study the latest bioinformatic knowledge.
From Japan, there were 10 attendees with the Korean and Chinese researchers of Bioinformatics field and were lectured and joined practical works in English. From DDBJ, Drs. Gojobori, Tateno, Saitou and Ikeo had joined as lectureres and staffs.


All members Dr. Gojobori lectured on "H-INV" and "GNP" At the lecture room
The JKC Bioinformatics Training course is held in Japan, Korea or China (rotaiting among 3 countries). In 2010, the course will be held in China, almost in the same season.
  

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