DDBJ Center News Archive

News from 1998

Publication of the C. elegansgenome sequence

The C. elegans sequencing project has completed the fifteen year project to sequence the complete genome of the nematode worm Caenorhabditis elegans (about 97 million bp). This project is a collaboration betweenthe Sanger Centre, Hinxton Hall, Cambridge and the Genome Sequencing Center at the Washington University School of Medicine, St. Louis. It was published on Science Vol. 282 No, 5396, pp. 2011-2046.
These sequence data were submitted to the DDBJ/EMBL/GenBank International Nucleotide Sequence Database. You can search those data through the DDBJ WWW server.
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About Release 36.0 and 37.0: a new system of "Nucleotide Sequence ID" and "Protein ID"

December 21,1998
DDBJ, EMBL, and GenBank have agreed to introduce a new system of identifiers for both nucleotide and protein sequences. The form of "Nucleotide Sequence ID" is 'Accession No. + Version No' (e.g., AB123456.1), "Protein ID" is 'CDS ID + Version No.'.
The accession portion of these identifiers is stable and will not change, but the version portion will be incremented whenever the underlying sequence changes. DDBJ, EMBL, and GenBank plan to synchronize their release-processing schedules so that a common close-of-data occurs on March 20, 1999. In DDBJ's case, we will advance date of close-of-data for Release 36.0 and 37.0, and put this system into operation from Release 37.0. Next release (Release 36.0) will be released at the
begeinning of January and Release 37.0 will be released in March.
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Announcement about the New Year Holiday of DDBJ

December 15,1998
We at DDBJ will suspend our business during the New Year Holiday from Dec. 29, 1998 to Jan. 3, 1999. We will stop most activities including issuing the accession numbers during the period, and resume the normal business on Jan 4 , 1999.
Thank you very much for your cooperation.
We wish you a Happy New Year.

DNA Data Bank of Japan
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DDBJ started to accept data submissions prepared by using Sequin 2.60

December 14,1998
Sequin is a stand-alone software tool developed by NCBI for submitting entries to the GenBank, EMBL, or DDBJ sequence databases. Sequin version 2.60 for Macintosh, PC/MS Windows, and Unix Computers are available from the DDBJ ftp site.
Please refer tohttp://www.ddbj.nig.ac.jp/sequin/index.html for details about sequin.
(Attention: Although the latest version of Sequin is 2.70, please use version 2.60 when you submit your data to DDBJ.)
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PDB Release 85 was released

December 01,1998
The Protein Data Bank (PDB) Release 85 was released on line to the public on Dec. 1, 1998 at DDBJ. PDB Release 85 consists of 8,112 entries.
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CAMUS Database is developed by DDBJ

November 30,1998
A new service called CAMUS Database is now available in DDBJ WWW site. This system constructed Compressed database for homology searches and Multiple-aligned Sequence Database.
The URL is http://wolf.genes.nig.ac.jp/camus/.This has a link from [Database Searches and Data Analyses] and [Links to Other Databases] of DDBJ Home Page.
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GIB; Rickettsia prowazekii and new function

November 18,1998
The Genome Inforamtion Broker (GIB) now includes the data of Rickettsia prowazekii.
In addition, a new function to search 19 genomes at once either by ORFs/genes/productsis or BLAST is now available.
You can find them from http://mol.genes.nig.ac.jp/gib/ .
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supernig periodic maintenance

November 17,1998
It happens in the following date, and be lets the service of supernig be suspended for the periodic maintenance of supernig.
1998.11/27(Fri) 12:00 - 21:00
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GenBank Rel.109, DAD Rel.5, PDB Rel.84 were released

November 13,1998
GenBank Release 109, DDBJ amino acid database (DAD) Release 5, PDB Release 84 were released on Nov. 13, 1998 at DDBJ. GenBank Release 109 consists of 2,837,897 entries, and the total number of bases reached 2,008,761,784. DAD Release 5 consists of 343,271 entries, and the total number of residues reached 105,546,945. PDB Release 84 consists of 7,578 entries.
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Dear DDBJ submitters

November 11,1998
We will change the contents of the e-mail informing you of the release of your submitted data as of November 16. The flat file of your sequence will not be attached to it. Thank you for your understanding.
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DDBJ Release 35 Completed

October 30,1998
The nucleotide sequence database collected and maintained by DDBJ is quarterly released on line to the public and distributed in the magnetic media. We completed DDBJ Release 35 in Oct. 1998. DDBJ Release 35 consists of 2,759,261 entries, and the number of bases reached 1,957,341,169.
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Announcement; network services in NIG Oct. 26, 1998

October 26,1998
All network services in DDBJ will be stopped becuase of a scheduled power cut at NIG.
from November 6 (Fri) 17:00
until November 7 (Sat) 20:00
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Termination of GDB Project

October 13,1998
The Genome Database project (GDB),which provides human gene mapping data to human genetics researchers from its base at Johns Hopkins School of Medicine, has ceased its operations.
This action is a consequence of the decision by the project's primary funder, the U.S. Department of Energy's Office of Energy Research, to discontinue GDB funding in order to focus its informatics resources primarily on the results of the sequencing phase of the Human Genome Project.
The database will continue to be made available to the scientific community till January 31, 1999.The extension is to provide a smooth transition of the database to the Computational Biosciences at the Oak Ridge National Laboratory (ORNL).
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Announcement concerning SWISS-PROT

October 13,1998
SWISS-PROT is an annotated protein sequence database and maintained collabor atively by Amos Bairoch at the Department of Medical Biochemistry of the Univers ity of Geneva and EBI (The European Bioinformatics Institute).In April this year, the SWISS-PROT group in Geneva joined a new academic institution, the Swiss Institute of Bioinformatics (SIB).
Starting in September 1998, SWISS-PROT intend to implement a system of an annual subscription fee for commercial use of the database. Both SIB and EBI mandated a new company, Geneva Bioinformatics (GeneBio) to act as their representative for the purpose of concluding the necessary license agreements and levying the fees.
Please refer to the following addresses for more information.
- EBI (http://www.ebi.ac.uk/sprot/summary.html)
- GeneBio (http://www.genebio.com/)
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LIBRA I updates

October 12,1998
A computer application of threading: LIBRA I was improved. We enlarged the size of the structural library about 400 to 1,400 structures. Also the form of the reply mail was somewhat revised: the protein name was informed as well as the PDB codes etc.
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DDBJ staff's publication on Bioinformatics

October 06,1998
DDBJ staff published on Bioinformatics.
Okayama, T., Tamura, T., Gojobori, T., Tateno, Y., Ikeo, K., Miyazaki, S., Fukami-Kobayashi, K. and Sugawara, H. (1998).
Formal design and implementation of an improved DDBJ DNA database with a new schema and object oriented library. Bioinformatics Vol. 14/6, 472-478.
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Homology search and analysis system updates

September 22,1998
DDBJ is operating FASTA, BLAST, SSEARCH homology search systems and
clustalw analysis system in WWW. Some new functions were recently added.
- Making connection from FASTA/BLAST to clustalw, FASTA/BLAST retrieved sequences can be used on clustalw.
- The result of clustalw can be shown on WWW.
- Information about phylogenic trees (dnd, tree, bootstrap) can be shown in graphically using by TreeView in clustalw.
(You need to install TreeView software in your computer to see phylogenic trees. )
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Retrieval System of Protein Mutant Database (PMD)

September 14,1998
The powerful retrieval system ofProtein Mutant Database(PMD) is now available, which is integrated with sequence and tertiary structure databases.
The user can retrieve PMD entries with any query keywords and amino acid sequences.
A 3D structure is displayed to show mutation sites in a different color.
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DDBJ Release 33 Completed

July 24,1998
The nucleotide sequence database collected and maintained by DDBJ is quarterly released on line to the public and distributed in the magnetic media. We completed DDBJ Release 33 in April 1998. DDBJ Release 33 consists of 2,174,769 entries, and the number of bases reached 1,479,303,279. Comparing to Release 29 that was released one year ago, the number of entries and bases increased by 71% and 82%, respectively.
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DDBJ Release 34 Completed

July 23,1998
The nucleotide sequence database collected and maintained by DDBJ is quarterly released on line to the public and distributed in the magnetic media. We completed DDBJ Release 34 in July 1998. DDBJ Release 34 consists of 2,412,785 entries, and the number of bases reached 1,708,580,623.
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Treponema pallidum and Chlamydia trachomatis Genome

July 22,1998
The Genome Inforamtion Broker (GIB) now includes the data of Treponema pallidum and Chlamydia trachomatis.
You can find them from here.
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July 15,1998
It happens in the following date, and be lets the service of supernig be suspended for the periodic maintenance of supernig.
1998.7.24 ( Fri) 12:00 - 21:00
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