DNA Data Bank of Japan

What's New 2002

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Copyright © 1995-2006
DDBJ All rights reserved.
PRF Rel. 88 was released Dec. 27, 2002
PRF (Protein Research Foundation)/SEQ database Release 88 was released on Dec. 27, 2002 at DDBJ. PRF Release 88 consists of 213,858 entries, and the total number of residues reached 76,590,687.
 
Genome sequence data was added to GIB Dec. 27, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Vibrio vulnificus CMCP6, Pseudomonas putida KT2440 and Bradyrhizobium japonicum USDA110 were released, we incorporated it to GIB, and now you can search those data.
- Vibrio vulnificus CMCP6
  Institute: Chonnam National University Medical College
  Reference: Complete genome sequence of Vibrio vulnificus CMCP6, Unpublished
- Pseudomonas putida KT2440
  Institute: TIGR
  Reference: Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440, Environ. Microbiol. 4 (12), 799-808 (2002)
- Bradyrhizobium japonicum USDA110
  Institute: Kazusa DNA Research Institute
  Reference: Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110, DNA Res. (2002) In press
 
Minerva periodic maintenance Dec. 17, 2002
Minerva service will be unavailable during the following date because of the periodic maintenance. Thank you very much for your understanding and cooperation.
Dec. 20 (Fri) 10:00- 21:00
 
Escherichia coli CFT073 was added to GIB Dec. 17, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Escherichia coli CFT073 was released, we incorporated it to GIB, and now you can search those data.
Institute: University of Wisconsin
Reference: Extensive Mosiac Structure Revealed by the Complete Genome Sequence of Uropathogenic Escherichia coli, Proc. Natl. Acad. Sci. U.S.A. (2002)
 
DDBJ Rel. 52 Completed Dec. 13, 2002
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public. We completed DDBJ Release 52 in Dec. 2002. DDBJ Release 52 consists of 20,354,812 entries, and the number of bases reached 26,931,456,316.
 
Mycoplasma penetrans HF-2 was added to GIB Dec. 13, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Mycoplasma penetrans HF-2 was released, we incorporated it to GIB, and now you can search those data.
Institute: NIH-NET
Reference: The complete genomic sequence of Mycoplasma penetrans, an intracellular bacterial pathogen in humans., Nucleic Acids Res. 30, 5293-5300 (2002)
 
Suspension of the DDBJ activity during the New Year Holidays Dec. 9, 2002
We at DDBJ will suspend our business for receiving and releasing data during the New Year Holidays from December 28th, 2002 to January 5th, 2003.
We will resume the normal business on January 6th, 2003.
Please note in particular that SAKURA will stop in operation from December 27th, 2002 to January 5th, 2003 and the new daily update will not release from December 28th to January 6th, 2003.
Thank you very much for your understanding and cooperation.
We wish you a Merry Christmas and Happy New year.
 
DNA Data Bank of Japan
 
59,971 full-length mouse cDNAs with functional annotation and huge scale 766,243 ESTs have been made public Dec. 5, 2002
Sequences of huge scale EST and full-length cDNA of Mus musculus have been registered to DDBJ by Dr. Y. Hayashizaki (Project Director)'s group at the RIKEN (The Institute of Physical and Chemical Research) Genomic Sciences Center. We assigned accession numbers to full-length cDNA 40,803 entries in the HTC division of the DDBJ/EMBL/GenBank International Nucleotide Sequence Database, and to EST 766,243 entries. The total numbers of mouse full-length cDNA was 59,971 entries by this submission.
All HTC entries have functional annotation assigned on the FANTOM2 (Functional ANnoTation Of Mouse) meeting held by Dr. Y. Hayashizaki group. We have released 766,243 ESTs records and, newly 40,803 entries of and 19,168 entries with updated annotation of HTC division records.
The accession numbers of the distributed entries are as below;
[HTC]
Updated entries: AK002213-AK018700, AK018701-AK021412, AK027261-AK027262
Newly entries: AK027903-AK054560, AK075567-AK090394, AK117103-AK117104
(Some of them are unpublished)
[EST]
Newly entries。ァBY000001-BY766243
Quality score (Phrap score) for all HTC entries including the updated records have been co-distributed.
The sequences were also published in Nature 420, 563-573, 2002 (5/12/2002).
 
Minerva service temporary down (today! Nov.29, 15:00-17:00) Nov. 29, 2002
Minerva service will be unavailable today because of the maintenance. Thank you very much for your understanding and cooperation.
 
Shewanella oneidensis MR-1 was added to GIB Nov. 28, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Shewanella oneidensis MR-1 was released, we incorporated it to GIB, and now you can search those data.
Institute: TIGR
Reference: Genome sequence of the metal-reducing bacterium, Shewanella oneidensis, Nat. Biotechnol. 20(11) 1118-1123(2002)
 
Wigglesworthia brevipalpis was added to GIB Nov. 26, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Wigglesworthia brevipalpis was released, we incorporated it to GIB, and now you can search those data.
Institute: Kitasato University
Reference: Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia, Nat. Genet. 32 (3), 402-407(2002)
 
DAD rel. 21 was released Nov. 20, 2002
DDBJ amino acid database (DAD) Release 21 was released on Nov. 20, 2002 at DDBJ. DAD Release 21 consists of 1,139,458 entries, and the total number of residues reached 349,308,832. The modification from this release is as follows:
1) TPA data file is added
2) The format of LOCUS line is changed
3) Information for location of intron is added
 
Corynebacterium efficiens YS-314 was added to GIB Nov. 15, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Corynebacterium efficiens YS-314 was released, we incorporated it to GIB, and now you can search those data.
Institute: NITE
Reference: The entire genomic sequence of Corynebacterium efficiens YS-314, Published Only in Database(2002)
 
Updates of "Conference on information biology" Nov. 11, 2002
Following conference was added to "Conference on information biology".
 
NIG Network service temporary down Nov. 8, 2002
NIG (National Institute of Genetics) network service will be unavailable during the following date because of the network maintenance. You can't use DDBJ network service. Thank you very much for your understanding and cooperation.
Nov. 15 (Fri) 17:00 - Nov. 16 (Sat) 22:30
 
The number of entries reached 20 million! Nov. 8, 2002
The number of entries distributed from DDBJ/EMBL/GenBank International Nucleotide Sequence Database reached 20 million on November 3.
Total number of entries (Nov.3): 20,026,341
Total number of nucleotides (Nov. 3): 26,716,227,080 bp
 
NIG Network service temporary down
NIG (National Institute of Genetics) network service will be unavailable during the following date because of the network maintenance. You can't use DDBJ network service. Thank you very much for your understanding and cooperation.
Nov. 6(WED), 2002 18:30-21:30
 
PIR rel. 74 was released Oct. 29, 2002
PIR rel. 74 was released on Oct. 29, 2002 at DDBJ. PIR rel. 74 consists of 283,227 entries, and the total number of residues reached 96,134,583 aa.

Streptococcus mutans UA159 was added to GIB Oct. 28, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Streptococcus mutans UA159 was released, we incorporated it to GIB, and now you can search those data.
Institute: University of Oklahoma Health Sciences Center
Reference: Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogen, Proc. Natl. Acad. Sci. U.S.A. 99 (22), 14434-14439 (2002)

Shigella flexneri, 2a 301 and Leptospira interrogans serovar lai str. 56601 were added to GIB Oct. 25, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Shigella flexneri, 2a 301 and Leptospira interrogans serovar lai str. 56601 were released, we incorporated it to GIB, and now you can search those data.
- Shigella flexneri, 2a 301
  Institute: Microbial Genome Center of Chinese Ministry of Public Health
  Reference: Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157, Nucleic Acids Res. 30 (20), 4432-4441 (2002)
- Leptospira interrogans serovar lai str. 56601
  Institute: Chinese National Human Genome Center at Shanghai(CHGC)

Brucella suis 1330 was added to GIB Oct. 18, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Brucella suis 1330 was released, we incorporated it to GIB, and now you can search those data.
Institute: The Institute for Genomic Researc
Reference: The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts, Proc. Natl. Acad. Sci. U.S.A. 99, 13148-13153 (2002)

Updates of "Conference on information biology" Oct. 16, 2002
Following conference was added to "Conference on information biology".

Streptococcus agalactiae NEM316 was added to GIB Oct. 7, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Streptococcus agalactiae NEM316 was released, we incorporated it to GIB, and now you can search those data.
Institute: Institut Pasteur
Reference: Genome sequence of Streptococcus agalactiae, a pathogen causing invasive neonatal diseases, Mol.Microbiol. 45(6), 1499-513(2002)

Updates of "Conference on information biology" Oct. 4, 2002
Following conferences were added to "Conference on information biology".

Bifidobacterium longum NCC2705 was added to GIB Oct. 3rd, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Bifidobacterium longum NCC2705 was released, we incorporated it to GIB, and now you can search those data.
Institute: Nestle Research Center
Reference: The Genome Sequence of Bifidobacterium longum Reflects its Adaptation to the Human Gastrointestinal Tract, Unpublished

DDBJ network services reopening Sep. 27, 2002
We resumed following DDBJ network services. Thank you very much for your understanding and cooperation.
[Homology search, clustalw, SRS, getentry, FTP]

Network service temporary down Sep. 26, 2002
Following DDBJ network services are suspended temporarily because of the server trouble. The service will be resumed in a few days. Thank you very much for your understanding and cooperation.
[homology search, clustalw, SRS, getentry, FTP]

URL change of getentry Sep. 25, 2002
The URL of [getentry] on DDBJ Homepage will be changed on October 1, 2002. New URL is as follows.
    English : http://getentry.ddbj.nig.ac.jp/
    Japanese: http://getentry.ddbj.nig.ac.jp/top-j.html
Presently, you can access to both new and old URLs. But, old URL will be stopped on January 31, 2003. So, please update your bookmarks and links, and setting of links to individual DDBJ entries using old URL to new URL.
This change was caused by the change of the port number from #8000 to the standard port #80. Because of this change, troubles for accessing to [getentry] due to port number setting will be solved.
Thank you very much for your understanding and cooperation.

GIB maintenance Sep. 29, 2002
BLAST2 and FASTA3 services of GIB will be unavailable during the following date because of the machine maintenance. Thank you very much for your understanding and cooperation.
Sep. 26 (Thu) 14:00-16:00 JST

DDBJ Rel. 51 Completed Sep. 24, 2002
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public and distributed in the magnetic media. We completed DDBJ Release 51 in Sep. 2002. DDBJ Release 51 consists of 18,401,358 entries, and the number of bases reached 22,782,404,136.
The format of LOCUS line in the flat file is changed as shown below to adjust to the GenBank format from the present release.
Present (rel. 51-):
  LOCUS AB000001 660 bp DNA linear PLN 01-FEB-2001
Old (-rel. 50):
  LOCUS AB000001 660 bp DNA PLN 01-FEB-2001

Annotation jamboree "H-Invitational" was held Sep. 13, 2002
Human Full-Length cDNA Annotation Invitational (H-Invitational) was held in Odaiba Tokyo, from Aug. 25 to Sep. 3.
120 researchers (domestic and foreign) assembled to annotate human full-length cDNA for the construction of the database expected to be useful for various biological field. This meeting was co-organized by JBIRC and DDBJ, and 9 researchers in NIG and 4 annotators attended as DDBJ members.
The report of this meeting was published in Nature 419, 3-4.

Updates of "Conference on information biology" Sep. 10, 2002
Following conference was added to "Conference on information biology".

Streptococcus agalactiae serotype V was added to GIB Sep. 2nd, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Streptococcus agalactiae serotype V was released, we incorporated it to GIB, and now you can search those data.
Institute: TIGR
Reference: Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae, Proc. Natl. Acad. Sci. U.S.A. 99 (2002) In press

Updates of "Conference on information biology" Sep. 2, 2002
Following conference was added to "Conference on information biology".

Updates of "Conference on information biology" Aug. 29, 2002
Following conferences were added to "Conference on information biology".

Thermosynechococcus elongatus BP-1 was added to GIB Aug. 22, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Thermosynechococcus elongatus BP-1 was released, we incorporated it to GIB, and now you can search those data.
Institute: Kazusa DNA Research Institute
Reference: Complete genome structure of the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1, DNA Res. (2002) In press

Updates of "Conference on information biology" Aug. 22, 2002
Following conferences were added to "Conference on information biology".

PRF Rel. 86 was released Aug. 20, 2002
PRF (Protein Research Foundation)/SEQ database Release 86 was released on Aug. 20, 2002 at DDBJ. PRF Release 86 consists of 205,029 entries, and the total number of residues reached 73,677,986.

Supernig periodic maintenanceAug. 15, 2002
Supernig service will be unavailable during the following date because of the periodic maintenance. Thank you very much for your understanding and cooperation.
Aug. 23 (Fri) 9:00-22:00

"S & W SEARCH" was released Aug. 7, 2002
DDBJ released a new homology search service "S&W SEARCH" on DDBJ web site. S&W SEAECH is based on Smith-Waterman algorithm, and characteristic in high-speed search (search time: within a few minutes) comparing with the present SSEARCH (several hours).
This service is available from [Homology Search] of DDBJ Home Page. You can use this program through the web site or e-mail, and the result is returned by e-mail. If you need an instruction document, you can obtain it by sending an e-mail to swsearch@nig.ac.jp, writing "help-e" on the mail body. Please use it.

Updates of "Conference on information biology" Aug. 6, 2002
Following conference was added to "Conference on information biology".

PIR rel. 73 was released Aug. 5th, 2002
PIR rel. 73 was released on Aug. 5th, 2002 at DDBJ. PIR rel. 73 consists of 283,239 entries, and the total number of residues reached 96,148,892 aa.

Yersinia pestis KIM was added to GIB Aug. 2nd, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Yersinia pestis KIM was released, we incorporated it to GIB, and now you can search those data.
Institute: University of Wisconsin
Reference: Genome Sequence of Yersinia pestis KIM, J. Bacteriol. 184 (16), 4601-4611 (2002)

Streptococcus pyogenes MGAS315 was added to GIB Jul. 22, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Streptococcus pyogenes MGAS315 was released, we incorporated it to GIB, and now you can search those data.
Institute: NIAID
Reference: Genome sequence of a serotype M3 strain of group A Streptococcus: Phage-encoded toxins, the high-virulence phenotype, and clone emergence, Proc. Natl. Acad. Sci. U.S.A. 99 (15), 10078-10083 (2002)

Updates of "Conference on information biology" Jul. 22, 2002
Following conference was added to "Conference on information biology".

Updates of "Conference on information biology" Jul. 19, 2002
Following conferences were added to "Conference on information biology".

Minerva periodic maintenance Jul. 12, 2002
Minerva service will be unavailable during the following date because of the periodic maintenance. Thank you very much for your understanding and cooperation.
Jul. 19 (Fri) 10:00- 22:00

"Overview of International Nucleotide Sequence Databases Policies" Jul. 11, 2002
Overview of International Nucleotide Sequence Databases Policies" was added to "Data Submission" page.

"Lib score (prediction of MHC binding peptides)" was released Jul. 9, 2002
DDBJ released a new service "Lib score (prediction of MHC binding peptides)" on DDBJ web site. The program was developed by Dr. Keiko Udaka, Kyoto University.
Usage is as follows: Choose an MHC molecule and enter an amino acid sequence in one-letter code. Click "execute" button and you will get the scores back. This service is available from [Protein Database and Structure] of DDBJ Home Page. Please use it.

Chlorobium tepidum TLS was added to GIB Jul. 4, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Chlorobium tepidum TLS was released, we incorporated it to GIB, and now you can search those data.
Institute: TIGR
Reference: The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium, Proc. Natl. Acad. Sci. U.S.A. (2002) In press

Buchnera aphidicola Sg (Schizaphis graminum) was added to GIB Jul. 3rd, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Buchnera aphidicola Sg (Schizaphis graminum) was released, we incorporated it to GIB, and now you can search those data.
Institute: University of Uppsala
Reference: 50 million years of genomic stasis in endosymbiotic bacteria, Science 296 (5577), 2376-2379 (2002)

Updates of "Conference on information biology" Jul.2nd, 2002
Following conference was added to "Conference on information biology".

SRS service reopening Jun. 28, 2002
We resumed the DDBJ SRS keyword search searvice, which stopped from June 26 for the maintenance. We appreciate your cooperation.

SRS service temporary down Jun. 26, 2002
DDBJ SRS keyword search searvice will be unavailable from today because of the maintenance. The service will be resumed in a few days. Thank you very much for your understanding and cooperation.

DAD rel. 20 was released June 26, 2001
DDBJ amino acid database (DAD) Release 20 was released on June 26, 2002 at DDBJ. DAD Release 20 consists of 1,062,430 entries, and the total number of residues reached 325,626,765.

SINET network service temporary down Jun. 21, 2002
NIG (National Institute of Genetics) network service will be unavailable during the following date because of the SINET network maintenance.
Thank you for your understanding and cooperation.
Jun. 27 (THU) 12:30pm-12:45pm
Jun. 29 (SAT) 12:30pm-12:40pm

DDBJ Rel. 50 Completed Jun.18, 2002
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public and distributed in the magnetic media. We completed DDBJ Release 50 in Jun. 2002. DDBJ Release 50 consists of 17,260,693 entries, and the number of bases reached 20,158,357,982.

Updates of "Conference on information biology" Jun. 7, 2002
Following conference was added to "Conference on information biology".

Corynebacterium glutamicum ATCC 13032 was added to GIB May 7, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Corynebacterium glutamicum ATCC 13032 was released, we incorporated it to GIB, and now you can search those data.
Institute: Kyowa Hakko Kogyo Co. Ltd.
Reference: Complete genomic sequence of Corynebacterium glutamicum ATCC 13032, Unpublished (2002)

Staphylococcus aureus MW2 was added to GIB Jun. 5, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Staphylococcus aureus MW2 was released, we incorporated it to GIB, and now you can search those data.
Institute: National Institute of Technology and Evaluation (NITE)
Reference: Genome and virulence determinants of high virulence community-acquired MRSA, Lancet 359, 1819-1827 (2002)

Updates of "Conference on information biology" Jun. 3rd, 2002
Following conferences were added to "Conference on information biology".

Over two billion bases released ! May 30, 2002
DDBJ construct nucleotide sequence database in accordance with the international rule among DDBJ/EMBL/GenBank. This database is updated everyday. The total number of released bases reached two billion on May 28.
- As of May 28, 2002
The total number of released bases 20,034,081,266 (17,240,418 entries)

Methanosarcina mazei Goe1, Xanthomonas campestris pv. campestris ATCC 33913 and Xanthomonas axonopodis pv. citri 306 were added to GIB May 30, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Methanosarcina mazei Goe1 , Xanthomonas campestris pv. campestris ATCC 33913 and Xanthomonas axonopodis pv. citri 306 were released, we incorporated them to GIB, and now you can search those data.
Methanosarcina mazei Goe1
  Institute: Goettingen Genomics Laboratory
  Reference: The genome of Methanosarcina mazei: Evidence for lateral gene transfer between Bacteria and Archaea, J. Mol. Microbiol. Biotechnol. (2002) In press
Xanthomonas campestris pv. campestris ATCC 33913 and
Xanthomonas axonopodis pv. citri 306
  Institute: University of Sao Paulo
  Reference: Comparison of the genomes of two Xanthomonas pathogens with differing host specificities, Nature 417 (6887), 459-463 (2002)

DDBJ disclosed Whole Genome Shotgun (WGS) sequence data May 23, 2002
DDBJ disclosed Whole Genome Shotgun (WGS) sequence data submitted to and disclosed by GenBank and EMBL. Retrievable accession numbers by getentry and their origins are as follows (totally 400,000 entries). Please note that accession numbers of WGS entries are 12 digits (4 digits alphabets + 8 digits numbers), different from ordinal DNA sequence entries.
    a_gambiae.strain : AAAB01000001 - AAAB01069724
    o_sativa.cultivar : AAAA01000001 - AAAA01103044
    mus_musculs : CAAA01000001 - CAAA01224713

Following files are also available from anonymous-ftp (ftp://ftp.ddbj.nig.ac.jp/ddbj_database/wgs/)
    a_gambiae.strain_PEST.gz (69,724 entries)
    o_sativa.cultivar_indica.gz (103,044 entries)
    mus_musculs.gz (224,713 entries)

Improvement of "get-entry" e-mail service May 22, 2002
"getentry" is a prompt search system by use of accession numbers and the like. You can now ask the e-mail server for 10-50,000 entries at once. Please send "help" to get-entry@nig.ac.jp and capture the manual.

Streptomyces coelicolor A3(2) and Thermoanaerobacter tengcongensis MB4T were added to GIB May 17, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Streptomyces coelicolor A3(2) and Thermoanaerobacter tengcongensis MB4T were released, we incorporated them to GIB, and now you can search those data.
Streptomyces coelicolor A3(2)
Institute: The Sanger Centre
Reference: Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2), Nature 417, 141-147(2002)
Thermoanaerobacter tengcongensis MB4T
Institute: Institute of Genetics and Development, Chinese Academy of Sciences
Reference: A Complete Sequence of T. tengcongensis Genome, Genome Res. 12 (5), 689-700 (2002)

The mouse genome draft sequence was made public May 16, 2002
The Mouse Genome Sequencing Consortium determined the mouse genome draft sequence. The data was submitted to GenBank, and released to public in DDBJ/EMBL/GenBank International Nucleotide Sequence Database on May 6. It covers 96% of the mouse genome.

DAD rel. 19 was released May 15, 2001
DDBJ amino acid database (DAD) Release 19 was released on May 15, 2002 at DDBJ. DAD Release 19 consists of 1,012,203 entries, and the total number of residues reached 309,708,601.

Announcement for DDBJ release May 10, 2002
-- A change of the periodical release schedule, a change of the compress format of "ddbjnew", addition of the new format files to DDBJ database --

A change of the periodical release schedule
The nucleotide sequence database collected and maintained by DDBJ is quarterly released to public. The present release is scheduled on January, April, July and October. DDBJ change them to March, June, September and December to avoid busy time for registration. Next periodical release is on June, one month earlier than the previously scheduled release time.
A change of the compress format of "ddbjnew"
To use the same compress format with GenBank and EMBL, DDBJ will change the compress format of the unified daily update file (ddbjnew) from "compress" to "gzip" which is superior to compress. The format of DDBJ periodical release has already changed to "gzip". The changeover of ddbjnew will start on May 29. Before that, DDBJ supply it by both formats on anonymous-ftp. Please be careful it you need to change the script.
Addition of the new format files to DDBJ database
DDBJ added new format databases on anonymous FTP since DDBJ release 49 (April 2002). Periodical release and unified daily update file (ddbjnew) can be retrieved by new format through the following anonymous FTP.
- FASTA format
  ftp://ftp.ddbj.nig.ac.jp/ddbj_database/ddbj/fasta/
- CDS sequence on FASTA format
  ftp://ftp.ddbj.nig.ac.jp/ddbj_database/ddbj/cdsdb/
DDBJ also provide XML formatted files through the anonymous FTP.
  ftp://ftp.ddbj.nig.ac.jp/ddbj_database/ddbj/xml/
  ftp://ftp.ddbj.nig.ac.jp/ddbj_database/ddbjnew/xml/

Minerva periodic maintenance May 10, 2002
Minerva service will be unavailable during the following date because of the periodic maintenance. Thank you very much for your understanding and cooperation.
May 17, (Fri) 12:00- 21:00

NIG network service temporary down May 8, 2002
NIG (National Institute of Genetics) network service will be unavailable during the following date because of the network maintenance. Thank you for your understanding and cooperation.
May 12 (Sun) 9:00-18:00

SINET network trouble is restored May 8, 2002
Due to the SINET network trouble, NIG network had been unable to use intermittently since March 29. It is restored. Thank you for your understanding.

Minerva service temporary down (today ! Apr. 26 ,17:00 pm-20:00pm) Apr. 26, 2002
Minerva service will be unavailable today because of the maintenance. Thank you very much for your understanding and cooperation.

Updates of "Conference on information biology" Apr.23, 2002
Following conference was added to "Conference on information biology".

DDBJ Rel. 49 Completed Apr. 19, 2002
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public and distributed in the magnetic media. We completed DDBJ Release 49 in Apr. 2002. DDBJ Release 49 consists of 16,503,157 entries, and the number of bases reached 18,579,627,226.

PIR rel. 72 was released Apr. 19, 2002
PIR Rel. 72 was released on Apr. 19, 2002 at DDBJ. PIR Rel. 72 consists of 283,175 entries, and the total number of residues reached 96,101,250 aa.

Guillardia theta, Leishmania major Friedlin and Plasmodium falciparum 3D7 were added to GIB Apr. 18, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Guillardia theta, Leishmania major Friedlin and Plasmodium falciparum 3D7 were released, we incorporated it to GIB, and now you can search those data.
Guillardia theta
Insititute: Institute for Marine Biosciences
Reference: Chloroplast protein and centrosomal genes, a tRNA intron, and odd telomeres in an unusually compact eukaryotic genome, the cryptomonad nucleomorph, Proc. Natl. Acad. Sci. U.S.A. 97 (1), 200-205 (2000)
Reference: The highly reduced genome of an enslaved algal nucleus, Nature 410 (6832), 1091-1096 (2001)
Leishmania major Friedlin
Insititute: Seattle Biomedical Research Institute
Reference: Leishmania major Friedlin chromosome 1 has an unusual distribution of protein-coding genes, Proc. Natl. Acad. Sci. U.S.A. 96 (6), 2902-2906 (1999)
The nucleotide sequence of Leishmania major Friedlin chromosome 1, Unpublished
Plasmodium falciparum 3D7
Insititute: The Institute for Genomic Research
Reference: Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum, Science 282 (5391), 1126-1132 (1998)

Updates of "Conference on information bi ology" Apr.18, 2002
Following conferences were added to "Conference on information biology".

PRF Rel. 84 was released Apr. 15, 2002
PRF (Protein Research Foundation)/SEQ database Release 84 was released on Apr. 15, 2002 at DDBJ. PRF Release 84 consists of 195,560 entries, and the total number of residues reached 70,303,296.

Fusobacterium nucleatum ATCC 25586 was added to GIB Apr. 10, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Fusobacterium nucleatum ATCC 25586 was released, we incorporated it to GIB, and now you can search those data.
Institute: Integrated Genomics
Reference: Genome Sequence and Analysis of the Oral Bacterium Fusobacterium nucleatum Strain ATCC 25586, J. Bacteriol. 184 (7), 2005-2018 (2002)

Methanosarcina acetivorance C2A was added to GIB Apr. 8, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Methanosarcina acetivorance C2A was released, we incorporated it to GIB, and now you can search those data.
Institute: Whitehead Institute
Reference: The genome of Methanosarcina acetivorans reveals extensive metabolic and physiological diversity, Genome Res. 12 (4), 532-542 (2002)

Fusobacterium nucleatum ATCC 25586, Streptococcus pyogenes MGAS8232 and Methanopyrus kandleri AV19 were added to GIB Apr. 5, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Fusobacterium nucleatum ATCC 25586, Streptococcus pyogenes MGAS8232 and Methanopyrus kandleri AV19 were released, we incorporated it to GIB, and now you can search those data.
Fusobacterium nucleatum ATCC 25586
Reference: Genome Sequence and Analysis of the Oral Bacterium Fusobacterium nucleatum Strain ATCC 25586, J. Bacteriol. 184 (7), 2005-2018 (2002)
Institute: Integrated Genomics

Streptococcus pyogenes MGAS8232
Reference: Genome sequence and comparative microarray analysis of serotype M18 group A Streptococcus strains associated with acute rheumatic fever outbreaks, Unpublished
Institute: NIAID

Methanopyrus kandleri AV19
Reference: The Complete Genome of the Hyperthermophile Methanopyrus kandleri AV19 and Monophyly of Archaeal Methanogens, Proc. Natl. Acad. Sci. U.S.A. 99 (7), 4644-4649 (2002)
Institute: Fidelity Systems, Inc

Network trouble Apr. 1st, 2002
Due to the SINET network trouble, NIG network has been unable to use intermittently since March 29. National Institute of Informatics is in charge of restoration. After the network is restored, we will announce it here. We apologize for the inconvenience and thank you for your understanding.

Schizosaccharomyces pombe 972h- was added to GIB Mar. 25, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Schizosaccharomyces pombe 972h- was released, we incorporated it to GIB, and now you can search those data.
Institute:The Sanger Centre
Reference: The genome sequence of Schizosaccharomyces pombe, Nature 415, 871-880 (2002)

Pyrococcus furiosus DSM 3638 was added to GIB Mar. 20, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Pyrococcus furiosus DSM 3638 was released, we incorporated it to GIB, and now you can search those data.
Institute: University of Utah
Reference: Genomic sequence of hyperthermophile, Pyrococcus furiosus: implications forphysiology and enzymology, Meth. Enzymol. 330, 134-157 (2001)

Updates of "Conference on information biology" Mar. 18, 2002
Following conferences were added to "Conference on information biology".

NIG network service temporary down Mar. 15, 2002
NIG (National Institute of Genetics) network service will be unavailable during the following date because of the network maintenance. Thank you for your understanding and cooperation.
Mar. 23 (Sat) 10:00-18:00

supernig periodic maintenance Mar. 15, 2002
Supernig service will be unavailable during the following date because of the periodic maintenance. Thank you very much for your understanding and cooperation.
Mar. 22 (Fri) 09:00-22:00

Open House on April 13th (Sat) ! Mar. 15, 2002
What is genes ? What is protein ? What is genome ? Why are we different from monkeys ? You will be able to find answers to these questions at our open house.

Implementation of XML technologies Mar. 15, 2002
CIB-DDBJ implemented SOAP and WSDL to improve the interoperability following the introductoin of DDBJ-XML. We also opened a relevant Web site is at http://www.xml.nig.ac.jp/

Updates of "Conference on information biology" Mar. 1st, 2002
Following conference was added to "Conference on information biology".

Japan - Korea Bioinformatics Training Course Feb. 26, 2002
We are so pleased to inform you that "Japan-Korea Bioinfomatics TrainingCourse" is held at the Center for Information Biology and DNA Data Bank ofJapan (CIB-DDBJ) in National Institute of Genetics on March 15-18, 2002. Please see HERE for more detailed information.
If you are interested in participating in this training course, please apply it now! Since the number of participants is limited to about 10 Japanese and 5 Korean students, the participants will be accepted on the basis of the first come the first service. Send your application to the following email address: nmurakat@genes.nig.ac.jp.

Updates of "Conference on information biology" Feb. 25, 2002
Following conferences were added to "Conference on information biology".

"DDBJ/CIB Human Genomics Studio" service reopening Feb. 18, 2002
We reopened "DDBJ/CIB Human Genomics Studio service. Thank you for your understanding and cooperation.

Updates of "Conference on information biology" Feb.18, 2002
Following conference was added to "Conference on information biology".

LIBRA updates Feb. 14, 2002
A computer application of threading: LIBRA I was improved. Structural library of LIBRA was enlarged to about 3,600 structures

Temporary stop of the "DDBJ/CIB Human Genomics Studio" Feb. 13, 2002
"DDBJ/CIB Human Genomics Studio" was suspended temporarily because of the server maintenance. It will recover in a week. Thank you very much for your understanding and cooperation.

Minerva periodic maintenance Feb. 12, 2002
Minerva service will be unavailable during the following date because of the periodic maintenance. Thank you very much for your understanding and cooperation.
Feb. 15 (Fri) 10:00 a. m. - 10:00 p. m.

Updates of "Conference on information biology" Feb.7, 2002
Following conference was added to "Conference on information biology".

PRF Rel. 83 was released Feb. 6, 2002
PRF (Protein Research Foundation)/SEQ database Release 83 was released on Feb. 6, 2002 at DDBJ. PRF Release 83 consists of 192,393 entries, and the total number of residues reached 69,036,298.

Updates of "Conference on information biology" Feb.4, 2002
Following conferences were added to "Conference on information biology".

DAD rel. 18 was released Jan. 30, 2002
DDBJ amino acid database (DAD) Release 18 was released on Jan. 30, 2002 at DDBJ. DAD Release 18 consists of 945,852 entries, and the total number of residues reached 290,665,398.

Clostridium perfringens 13 and Pyrobaculum aerophilum IM2 were added to GIB Jan. 25, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Clostridium perfringens 13 and Pyrobaculum aerophilum IM2 were released, we incorporated it to GIB, and now you can search those data.
Clostridium perfringens 13
Reference: Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater, Proc. Natl. Acad. Sci. U.S.A. 99, 996-1001 (2002) Institute: University of Tukuba
Pyrobaculum aerophilum IM2
Reference: Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum, Proc. Natl. Acad. Sci. U.S.A. 99 (2), 984-989 (2002) Institute: University of California, Los Angeles

Link to protein mutant database "PMD" was enhanced. Jan. 18, 2002
Link to PMD (Protein Mutant Database) is added at DDBJ web top page. This database is constructed by Laboratory for Gene-Product Informatics in National Institute of Genetics.
The URL is http://pmd.ddbj.nig.ac.jp/. This has a link from [Protein Database and Structure] of DDBJ Home Page.

DDBJ Rel. 48 Completed Jan. 18, 2002
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public and distributed in the magnetic media. We completed DDBJ Release 48 in Jan. 2002. DDBJ Release 48 consists of 15,016,100 entries, and the number of bases reached 16,197,713,855.

Updates of "Conference on information biology" Jan. 15, 2002
RECOMB 2002 (April 18-21, 2002), IN SILICO BIOLOGY (June 2-3, 2002) , BIOINFORMATICS & GENOME RESEARCH (June 4-5, 2002) , PROTEOMICS (June 6-7, 2002) , The 10th International Conference on Intelligent Systems for Molecular Biology (August 3-7, 2002) and The 3rd International Conference on Systems Biology (December 13-15, 2002) were added to "Conference on information biology".

Brucella melitensis 16M was added to GIB Jan. 7, 2002
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Brucella melitensis 16M was released, we incorporated it to GIB, and now you can search those data.
Institute: University of Scranton and Integrated Genomics
Reference: The genome sequence of the facultative intracellular pathogen Brucella melitensis, Proc. Natl. Acad. Sci. U.S.A. 99, 443-448 (2002)
 
 
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