DNA Data Bank of Japan
DDBJ Mail Magazine 
June.22, 2006
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Copyright © 1995-2006
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 ♦ Do you enjoy the season? 
This is the web version of the bimonthly DDBJ Mail Magazine (Number 26th).
It is getting increasingly warm and humid day by day. Do you have any plans for this summer season to enjoy outdoor activities?
If you have any questions and suggestions about DDBJmag, please don't hesitate to write to ddbjmag@ddbj.nig.ac.jp. We really want to hear from you!!!

 ♦ Professor Gojobori was elected as one of the Foreign Honorary Members of AAAS. 
Professor Takashi Gojobori (the Director of CIB) was elected as one of the Foreign Honorary Members of the AAAS (American Academy of Arts and Science) on April 22, 2006. This year the AAAS had selected 175 fellows and 20 foreign honorary members from various fields. Prof. Gojobori was recognized for his contribution to the fields of Evolutionary and Population Biology and Ecology.
The AAAS was founded in 1780 and since then, 4000 American fellows and 600 foreign members were invited as honorary members. It is considered great honor in the United States of America to become a fellow of this academy since members include some of the former U.S. Presidents and the Nobel Prize laureates.
Previously from the National Institute of Genetics, some pelple, such as Dr. Motoo Kimura and Dr. Tomoko Ota, were selected as honorary members of AAAS. However, from DDBJ, Prof. Gojobori becomes the first scientist to receive this honor. Dr. Gojobori has been also acknowledged as a Fellow of the American Association for Advancement of Science (AAAS) on last September, 2005.

 ♦ Whole genome data are available from GIB by FTP 
GIB (Genome Information Broker) is a comprehensive data repository of complete genomes of microorganisms and some eukaryote species. Currently, stores 352 complete genomes of archeal and bacterial species.
The genome sequence and annotation are download-able strain by strain from the top page of GIB and also can be accessed from the FTP download site that was opened to the public (ftp://ftpgib.genes.nig.ac.jp/).

 ♦ Update of databases related to the H-Invitational 
Recently, there has been a major update of the content of the H-Invitational database and related databases. The main updates are the following:
1. The number of cDNA entries has increased to167,992 from 56,419.
2. The number of LOCUS entries has increased to 35,005 from 25,585.
3. Version of mirror H-Invitational Database (H-InvDB)* become "3.0".
Databases related to the H-Invitational
H-Invitational Database CIB-DDBJ Flat File Server
Mirror H-Invitational Database(H-InvDB)


 ♦ The distribution of massive entries 
The massive sequence data which were collected by DDBJ and released through the INSD (International Nucleotide Sequence Database) from this January to March are as follows:
Release of additional human CAGE data (MGA entry)
DDBJ newly distributed 1.89 million entries of human originated short-transcript sequences as MGA (Mass sequence for Genome Annotation). Those data have been submitted by RIKEN Genome Sciences Center. All MGA entries can be downloaded from the DDBJ Anonymous FTP site (below) and a brief explanation of the published MGA data can be also found in the same URL.
Anonymous FTP
  • ftp://ftp.ddbj.nig.ac.jp/ddbj_database/mga/
  • Project_Index (Brief description of MGA data)
  • The related URL for this issue
  • Press release of RIKEN (Japanese only)
  • More about MGA entry
  • Release of new 223 thousands WGS entries of the Medaka strain Hd-rR
    DDBJ newly released 232 thousands WGS entries of the Medaka strain Hd-rR, which had been submitted by the University of Tokyo.
    Reference URL: http://medaka.utgenome.org/
    The accession numbers: BAAF02000001-BAAF02223025 (223025 entries)
    These entries were released as DDBJ daily updates on 4/19.
    All of the data can be retrieved at anonymous FTP site (Oryzias_latipes_WGS_060419_1.seq.gz).
    Release of new 31 thousands scaffold/CON entries of the Medaka strain Hd-rR
    DDBJ newly released 31 thousands scaffold/CON entries of the Medaka strain Hd-rR , which had been submitted by the University of Tokyo. They correspond to the Medaka WGS dataset released on 4/11.
    Reference URL: http://medaka.utgenome.org/
    The accession numbers: DF038236-DF069193 (30958 entries)
    These entries were released as DDBJ daily updates on 4/14.
    All of the data can be retrieved at anonymous FTP site (Oryzias_latipes_CON_060524_1.seq.gz).
    Release of new 232 thousands WGS entries of the Medaka strain Hd-rR
    DDBJ newly released 232 thousands WGS entries of the Medaka strain Hd-rR, which had been submitted by the University of Tokyo.
    Reference URL: http://medaka.utgenome.org/
    The accession numbers: BAAF01000001-BAAF01232667 (232667 entries)
    These entries were released as DDBJ daily updates on 4/11.
    All of the data can be retrieved at anonymous FTP site (Oryzias_latipes_WGS_060411_1.seq.gz).
    Release of new 243 thousands wheat EST entries
    DDBJ newly released 243 thousand wheat EST entries, which had been submitted by Kyoto Prefectural University.
    The accession numbers: CJ493525-CJ736986 (243462 entries)
    All of the data can be retrieved at anonymous FTP site. (Triticum_aestivum_EST_20060404_1.seq.gz)


     ♦ The 19th International Collaborative Meeting and International Advisory Committee were held at NCBI. 
    The International Nucleotide Sequence Database Collaboration (INSDC) have been developed and maintained between DDBJ, EMBL and GenBank since 1986. To promote its activities smoothly, we annually hold an International Collaborative meeting (ICM) and an Internatinal Advisory Committee (IAC). In this year, both meetings were held at NCBI (USA). The ICM took place from May 15th to17th, and several staffs and annotators from DDBJ attended this annual meeting, where they extensively discussed practical operations and various other issues related to the activities of INSDC.
    The IAM meeting was held from May 18th to 19th and some of the DDBJ staffs also participated in this meeting to discussed on general guidelines for the INSDC.
    We are going to post the Report of Collaborative meeting soon at DDBJ HP.

     ♦ New Statistics; Journal Ranking Top 100 
    From Release 65, we have added the list of "Journal Ranking 100 by entries/papers" to the Breakdown statistics. This list is based on the frequency of appearance of entries and papers from REFERENCE lines of the flat file in Release 65. For more information, please refer to "Breakdown statistics"

     ♦ DDBJ Rel. 65 Completed 
    The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public. We completed DDBJ Release 65 on March 30, 2006. DDBJ Release 65 consists of 55,890,995 entries, and the number of bases reached 60,564,721,635. Visit DDBJ FTP site for accessing new periodical release and download new data.
    DNA
    database
    Rel.DateDDBJ
    Date
    EntriesBases
    DDBJ6503/0603/0655,890,99560,564,721,635
    Protein
    database
    Rel.DateDDBJ
    Date
    SequencesResidues
    DAD3504/0604/062,984,526915,520,773
    UniProt7.705/0605/063,134,1871,023,776,867
    UniProt/Swiss-Prot49.705/0605/06219,36180,573,946
    UniProt/TrEMBL32.705/0605/062,914,826943,202,921
    PRF10803/0604/06555,007195,762,527
    PDB PDB site is weekly update and DDBJ
    check the data and daily update. (36,428 entries on May 16)
    * Date : Official released date written in the Release Note.
    * DDBJ date : the released date from DDBJ web page.
    * Rate of increase : increasing rate in comparison with the previous Release

    In addition, along with the Release 65, we updated the "Top 30 organisms of DDBJ current release(-Release 65)" in which Aedes aegypti (Dengue Mosquito) newly jumped into the Top list.

     ♦ Errata at DDBJ service 
    From the beginning of this May, there were several troubles which made our services be temporarily suspended. Since many of these problems happened during night time and weekends, the restoration of services was delayed and took long to be recovered. We deeply apologize for any inconveniences that this may have caused to our users.
    We will try to set the preventive measures to cope with such unexpected troubles immediately.

     ♦ DDBJ staff Column: At the 20th Anniversary of DDBJ 
    Professor Takashi Gojobori
    The National Institute of Genetics, CIB/DDBJ Director

    The research project of DDBJ preliminary started from the begging of 1980s. The official activities started from 1986, when the current CIB/DDBJ building was constructed at the NIG (National Institute of Genetics). As you may know, DDBJ have constructed the International Nucleotide Sequence Databases (INSD) in collaboration with EBI (EMBL) in Europe and NCBI (GenBank) in the US, and have been working together for twenty years.
    On this May 15-19, we hold the annual International collaborative meeting and advisory meeting at NIH. In this meeting, it was highlighted that as one of the international corporative research activities, the INSD activities were highly valued, and also evaluated as a successful model in the American research history.
    We really appreciate all the submitters of the data and the users who strongly have been supporting us.
    From now on, we will carry out coalition with other Asian countries and, as one of the responsible members of life science, actively cooperate with the government which plan to make the unification of databases.
    We sincerely ask for further support of each field and each district.



    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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    Last modified: Oct. 07, 2011