DDBJ Center News Archive

News from 2003

Updates of "Conference on information biology"

2003年12月26日
Following conferences was added to "Conference on information biology".
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DDBJ Rel. 56 Completed

December 24,2003
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public.We completed DDBJ Release 56 in Dec, 2003.DDBJ Release 56 consists of 30,405,173 entries, and the number of bases reached 36,079,046,032.
FTP site for periodical release and new data download
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Geobacter sulfurreducens PCA was added to GIB

December 22,2003
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.Because the genome sequence data of Geobacter sulfurreducens PCA was released, we incorporated it to GIB, and now you can search those data.
Institute: TIGR
Reference: Genome of Geobacter sulfurreducens: metal reduction in subsurface environments, Science 302 (5652),1967-1969 (2003)
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Supernig periodic maintenance

December 12,2003
Supernig service will be unavailable during the following date because of the periodic maintenance.
Thank you very much for your understanding and cooperation.
Dec. 19 (Fri) 12:00- 21:00
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Data were added to GIB

December 11,2003
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.
Because the genome sequence data of Rhodopseudomonas palustris CGA009 and Onion yellows phytoplasma were released, we incorporated it to GIB, and now you can search those data.
References (Institutes):
Rhodopseudomonas palustris CGA009 (JGI):
Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris, Unpublished.
Onion yellows phytoplasma (The University of Tokyo):
Reductive evolution suggested from the complete genome sequence of a plant-pathogenic phytoplasma, (er) Nature Genetics, 10.1038/ng1277 (2003)
Reductive evolution suggested from the complete genome sequence of a plant-pathogenic phytoplasma, Nature Genetics (2004) In press
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Suspension of the DDBJ activity during the New Year Holidays

December 09,2003
We at DDBJ will suspend our business for receiving and releasing data during the New Year Holidays from December 27th, 2003 to January 4th, 2004.
We will resume the normal business on January 5th, 2004.
Please note in particular that SAKURA will stop in operation from December 26th, 2003 to January 4th, 2004 and the new daily update will not be released from December 27th to January 5th, 2004.
Thank you very much for your understanding and cooperation.
We wish you a Merry Christmas and Happy New Year.
 
DNA Data Bank of Japan
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PRF Rel. 94 was released

December 05,2003
PRF (Protein Research Foundation)/SEQ database Release 94 was released on Dec. 5th, 2003 at DDBJ. PRF Release 94 consists of 239,691 entries, and the total number of residues reached 85,245,893.
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Change in "BASE COUNT line" of the DDBJ flat file

December 03,2003
The BASE COUNT line of the DDBJ flat file format will be changed from DDBJ release 56 (Dec. 2003), corresponding to the relaxation of the maximum sequence length restriction¡Ê350,000 bp/entry¡Ëin the entry that had been practised at DDBJ/EMBL/GenBank International Nucleotide Sequence Databases.
In the BASE COUNT line of the DDBJ flat file format, 6 digits had been allocated for each number of a, c, g, t and other bases in the sequence. Hereafter, in the new flat file format, 9 digits are allocated for each number of a, c, g and t, while the numbers of other bases are removed.
In accordance with the relaxation of sequence length limitation, GenBank had already dropped the BASE COUNT line from their flat file format from GenBank Release 138 (Oct. 2003).
We DDBJ have decided to maintain the BASE COUNT line in our flat file format from the view that GC contents are still important information to characterize the sequence.
Prior to publication of release 56 in December, 2003, the new DDBJ flat file format is adopted to daily data update from Dec. 3.

Following is an example of the new BASE COUNT line.
    = = = = = = = = example = = = = = = = =
    1    6   11   16   21   26   31   36   41   46   51   56   61   66   71
    |----|----|----|----|----|----|----|----|----|----|----|----|----|----|
    BASE COUNT    123456789 a    123456789 c    123456789 g    123456789 t

For detailed explanation of flat files of DDBJ format, please refer to Guidance for Nucleotide Sequence Data Submission to DDBJ (Guidance 10. Explanation of DDBJ flat file format)
If you have any questions about the change, please send an e-mail to ddbj@ddbj.nig.ac.jp.
Thank you very much for your understanding and cooperation.
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PIR rel. 78 was released

November 27,2003
PIR rel. 78 was released on Nov. 26, 3003 at DDBJ. PIR rel. 78 consists of 283,348 entries, and the total number of residues reached 96,183,374 aa.
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NIG Network service temporary down

November 21,2003
NIG (National Institute of Genetics) network service will be unavailable at the following schedule because of the planned blackout and network maintenance. DDBJ network service and NIG supercomputer (supernig and minerva) service will also be unavailable. Thank you very much for your understanding and cooperation.
Nov. 28(FRI) 17:00 - Nov. 29(SAT) 23:00
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The new phylum data was submitted to DDBJ

November 18,2003
Gemmatimonas aurantiaca, a new bacteria identified by
National Institute of Advanced Industrial Science and Technology (AIST) was approved as a new "Phylum" by ICSP*.
The new phylum name "Gemmatimonadetes" was appeared in Int. J. Syst. Evol. Microbiol. 53, 1155-1163 (2003) in this July. By this new approval, bacteria are classified into 24 phylums.
DNA data of Gemmatimonas aurantiaca had been submitted to DDBJ, and assigned an accession number AB072735. The data are available by DDBJ getentry.
Gemmatimonas aurantiaca
Lineage (full)
cellular organisms; Bacteria;
Gemmatimonadetes; Gemmatimonadetes (class);
Gemmatimonadales; Gemmatimonadaceae; Gemmatimonas
*ICSP: International Committee on Systematics of Prokaryotes
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Minerva temporarily down (today!)

November 12,2003
Minerva service will be unavailable today because of the maintenance. Thank you very much for your understanding and cooperation.
Nov. 12 18:00-20:00 (Today!)
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Corynebacterium diphtheriae gravis NCTC13129 was added to GIB

November 10,2003
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Corynebacterium diphtheriae gravis NCTC13129 was released, we incorporated it to GIB,
and now you can search those data.
Institute: Sanger Institure
Reference: The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129, Nucleic Acids Res. 31(22), 6516-6523(2003)
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Addition of download menu to GIB

November 07,2003
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.
New menu "List of gene name, GC %, and GC skew" was added to GIB chromosome and plasmid download site on Nov. 5. You can download GC % and GC skew of each gene at once.
Download menu also provides "Whole genome flat file (DDBJ or FASTA format)", "DNA sequences of all features (FASTA format)" and "Amino acid sequences of CDS (FASTA format)" etc. This menu appears in the left blue frame when the organism name was selected.
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Updates of "Conference on information biology"

November 05,2003
Following conferences was added to "Conference on information biology".
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Updates of "Conference on information biology"

October 28,2003
Following conferences were added to "Conference on information biology".
Services: ddbj Keywords:

DAD rel.25 and SWISS-PROT rel.42 were released

October 24,2003
DDBJ amino acid database (DAD) Release 25 and SWISS-PROT release 42 were released on Oct. 23, 2003 at DDBJ. DAD Release consists of 1,547,330 entries,and the total number of residues reached 478,115,729.
SWISS-PROT release consists of 135,850 entries, and the total number of residues reached 50,046,799.

FTP site for DB download
Services: ddbj Keywords:

Version-up of BLAST, FASTA, SSEARCH (forthcoming)

October 15,2003
BLAST, FASTA, SSEARCH of DDBJ homology search services provided through web and E-mail, are to be updated.Version information and update schedule are as follows.Service is not interrupted.
BLAST: 2.0.11 -> 2.2.6
FASTA: FASTA32t09 -> FASTA34t21
SSEARCH: FASTA32t09 -> FASTA34t21
Oct. 17, 2003 (Fri.) at 10:00 AM
 
User interface is not changed by this version-up, though there are some changes in the result forms for FASTA and SSEARCH.
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NIG Network service temporary down

October 15,2003
NIG (National Institute of Genetics) network service will be unavailable at the following schedule because of the network maintenance.DDBJ network service and NIG supercomputer (supernig and minerva) service will also be unavailable. Thank you very much for your understanding and cooperation.
Oct. 21 (TUE) 18:00- 22:00
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Vibrio vulnificus YJ016 was added to GIB

October 14,2003
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.Because the genome sequence data of Vibrio vulnificus YJ016 was released, we incorporated it to GIB, and now you can search those data.
Institute: National Yang Ming University
Reference: Comparative Genome Analysis of Vibrio vulnificus, a Marine Pathogen, Unpublished (2003)
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PRF Rel. 93 was released

October 09,2003
PRF (Protein Research Foundation)/SEQ database Release 93 was released on Oct. 9th, 2003 at DDBJ. PRF Release 93 consists of 236,775 entries, and the total number of residues reached 84,294,838.
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Chimpanzee Chromosome 22 genomic sequences released

October 07,2003
DDBJ (DNA Data Bank of Japan) released chimpanzee (Pan troglodytes) chromosome 22 genomic nucleotide sequence data on October 7.
Sequencing was conducted by the following eight institutions: two Japanese groups (RIKEN GSC and National Institute of Genetics), three German groups (Max Planck Institute for Molecular Genetics, German Center for Biotechnology, and Institute of Molecular Biotechnology), Chinese National Human Genome Center
at Shanghai, Korean Research Institute of Bioscience and Biotechnology (KRIBB), and National Yang-Ming University at Taipei.
Chimpanzee chromosome 22 corresponds to human chromosome 21, and determination of entire chromosomal genomic sequence is the first for non-human primates.
Accession numbers released from DDBJ are BS000001-BS000245. You can retrieve above entries via DDBJ getentry system:http://getentry.ddbj.nig.ac.jp/top-e.html
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Updates of "Conference on information biology"

October 07,2003
Following conferences was added to "Conference on information biology".
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Data were added to GIB

October 01,2003
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Gloeobacter violaceus PCC 7421 and Photorhabdus luminescens subsp. laumondii TTO1 were released, we incorporated them to GIB, and now you can search those data.
References (Institutes):
Gloeobacter violaceus PCC 7421 (Kazusa DNA Research Institute):Complete genome structure of Gloeobacter violaceus PCC 7421,a cyanobacterium that lacks thylakoids, DNA Res. 10, 137-145 (2003)
Complete genome structure of Gloeobacter violaceus PCC 7421, a cyanobacterium that lacks thylakoids (supplement), DNA Res. 10, 181-201 (2003)

Photorhabdus luminescens subsp. laumondii TTO1 (Institut Pasteur):
Complete genome sequence of the entomapathogenic bacterium Photorhabdus luminescens, Nat. Biotechnol. 11(1),(2003),Unpublished.
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NIG Network service temporary down

October 01,2003
NIG (National Institute of Genetics) network service will be unavailable at the following schedule because of the network maintenance. DDBJ network service and NIG supercomputer (supernig and minerva) service will also be unavailable. Thank you very much for your understanding and
cooperation.
Oct. 8 (Wed) 18:00- 22:00
Services: ddbj Keywords:

Statistics [Top 30 organisms according to the total number of nucleotides] Update

September 30,2003
Top 30 organisms according to the total number of nucleotides (- DDBJ rel.55) in DDBJ statistics was updated with releasing DDBJ Rel. 55.
Zea mays subsp. mays (corn) ranked in 28th, it was 77th at previous release.Click the organism name to view the graph of change.
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Scheduled stop of the GIB server

September 19,2003
GIB server will be stopped for a machine maintenance.
From Sep 26 (Fri) 13:00 pm to 18:00 pm
Thank you very much for your cooperation.
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DDBJ Rel. 55 Completed

September 19,2003

The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public.We completed DDBJ Release 55 in September 19, 2003.DDBJ Release 55 consists of 27,753,140 entries, and the number of bases reached 34,280,225,489.
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Updates of "Conference on information biology"

September 18,2003
Following conferences were added to "Conference on information biology".
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Wolinella succinogenes DSMZ 1740 was added to GIB

September 09,2003
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.Because the genome sequence data of Wolinella succinogenes DSMZ 1740 was released, we incorporated it to GIB, and now you can search those data.
Institute: Max-Plank Institut
Reference: Complete genome sequence and analysis of Wolinella succinogenes, Unpublished.
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Data were added to GIB

September 08,2003
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Chromobacterium violaceum ATCC 12472, and Porphyromonas gingivalis W83 were released, we incorporated them to GIB, and now you can search those data.
References (Institutes):
Chromobacterium violaceum ATCC 12472 (LNCC):The complete genome sequence of Chromobacterium violaceum, reveals remarkable and exploitable bacterial adaptability, Proc. Natl. Acad. Sci. U.S.A. (2003) In press
Porphyromonas gingivalis W83 (TIGR):Complete Genome Sequence of the Oral Pathogenic Bacterium Porphyromonas gingivalis Strain W83, J. Bacteriol. 185 (18), 5591-5601 (2003)
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[Homology Search] EST organism options change for DIVISION

September 05,2003
DDBJ provides homologous sequences search service by web site and e-mail.You can select organisms in the DIVISION to search effectively (this selection is valid only when "DDBJ ALL" or "DDBJ updates" is selected).
From September 11, 2003, number of EST organism options for DIVISION in the following services is changed from 31 to 22.We include some subspecies into higher rank species, and delete some organisms.
services: FASTA, BLAST, SSEARCH, S&W SEARCH
newly added organisms (EST):
Ciona intestinalis, Gallus gallus, Silurana tropicalis
deleted organisms (EST):
Bombyx mori, Brugia malayi, Leishmania major, Neurospora crassa, Onchocerca volvulus, Plasmodium falciparum, Rattus sp., Saccharomyces cerevisiae, Schistosoma mansoni, Schizosaccharomyces pombe, Sus scrofa, Trypanosoma cruzi
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Network service temporary down

August 29,2003
Following service will be unavailable during the following date because of the maintenance.
Thank you very much for your understanding and cooperation.
Sep. 1 (Mon) 18:00- 18:30
getentry, SRS, SQmatch, Data Retrieval by key words using SFgate & WAIS, Anonymous FTP
Services: ddbj Keywords:

Data were added to GIB

August 19,2003
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Prochlorococcus marinus MED4, Prochlorococcus marinus MIT9313, and Synechococcus sp. WH 8102 were released, we incorporated them to GIB, and now you can search those data.
References (Institutes):
Prochlorococcus marinus MED4 (JGI):
Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation, Nature [Epub ahead of print] (2003)

Prochlorococcus marinus MIT9313 (JGI):
Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation, Nature [Epub ahead of print] (2003)

Synechococcus sp. WH 8102 (JGI):
The genome of a motile marine Synechococcus, Nature [Epub ahead of print] (2003)
Services: ddbj Keywords:

S&W search service maintenance

August 18,2003
The return of S&W search results will be delayed due to a maintenance of the search engine from Aug 18 to Aug 19. Your request will be queued during this period.
Services: ddbj Keywords:

Minerva periodic maintenance

August 18,2003
Minerva service will be unavailable during the following date because of the periodic maintenance.
Thank you very much for your understanding and cooperation.
Aug. 22 (Fri) 12:00- 21:00
Services: ddbj Keywords:

Data were added to GIB

August 13,2003
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Candidatus Blochmannia floridanus,
Bordetella pertussis Tohama I, Bordetella parapertussis 12822 and
Bordetella bronchiseptica RB50 were released, we incorporated them to GIB, and now you can search those data.
References (Institutes):
Candidatus Blochmannia floridanus (University of Valencia): The genome sequence of Blochmannia floridanus: Comparative analysis of reduced genomes., Proc. Natl. Acad. Sci. U.S.A. 100, 9388-9393 (2003)
Bordetella pertussis Tohama I (Sanger Institute):
Comparative analysis of the genome sequences of Bordetella pertussis,
¡¡Bordetella parapertussis and Bordetella bronchiseptica. Nat. Genet. DOI, 10.1038/Ng1227-10.1038/Ng1227(2003).

Bordetella parapertussis 12822 (Sanger Institute):
Comparative analysis of the genome sequences of Bordetella pertussis,
¡¡Bordetella parapertussis and Bordetella bronchiseptica,
¡¡Nat. Genet. DOI, 10.1038/Ng1227-10.1038/Ng1227(2003).

Bordetella bronchiseptica RB50 (Sanger Institute):
Comparative analysis of the genome sequences of Bordetella pertussis,
¡¡Bordetella parapertussis and Bordetella bronchiseptica,
¡¡Nat. Genet. DOI, 10.1038/Ng1227-10.1038/Ng1227(2003).
Services: ddbj Keywords:

URL change of SFgate-WAIS

August 11,2003
SFgate-WAIS is data retrieval service by keywords provided on the DDBJ web. The URL of SFgate-WAIS will be changed from August 18, 2003.
New URL is:
  English http://dbsearch.ddbj.nig.ac.jp/dbsearch-e.html
  Japanese http://dbsearch.ddbj.nig.ac.jp/dbsearch-j.html
    (former URL: http://ftp2.ddbj.nig.ac.jp:8080/dbsearch-j-new.html)
Old URL will be stopped on Septembsr 16, 2003. So, please update your bookmarks and links. This change accompanies a change of the port number from current #8000 to new #80 (standard port).
Because of this change, troubles of accessing to SFgate-WAIS due to port number mismatch will be solved. Contents of the service has no change.
Thank you very much for your understanding and cooperation.
Services: ddbj Keywords:

URL change for ancient DNA database

August 08,2003
Ancient DNA Database (Ancient Genome Encyclopedia: AGE) is the database for ancient DNA, treating many information for DNA, such as extracted from human or animal bones which are excavated from ancient remains. This database is basically designed by Drs. Naruya Saitou, National Institute of Genetics, and
Shintaroh Ueda, The University of Tokyo, and maintained by DDBJ. The URL
was changed as follows:
New URL: ¡¡ http://www.ddbj.nig.ac.jp/aDNA/
(former URL:http://spinner.lab.nig.ac.jp/aDNA/)
Please change your bookmarks as necessary.
Services: ddbj Keywords:

S&W search service reopening

August 04,2003
We resumed S&W search service on Aug. 1. Thank you very much for your understanding and cooperation.
Services: ddbj Keywords:

S&W search service temporary down

July 29,2003
The S&W search service is unavailable because of the maintenance. Your request will be queued and the result will be returned after the maintenance.Thank you very much for your understanding and cooperation.
Services: ddbj Keywords:

NIG Network service temporary down

July 28,2003
NIG (National Institute of Genetics) network service will be unavailable at the following schedule because of the SINET network maintenance.
DDBJ network service and NIG supercomputer (supernig and minerva) service will also be unavailable. Thank you very much for your understanding and cooperation.
Aug. 8(FRI), 12:00-13:00 (15 minutes)
Services: ddbj Keywords:

Data were added to GIB

July 28,2003
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Chlamydophila pneumoniae TW-183, Haemophilus ducreyi 35000HP, and Prochlorococcus marinus subsp. marinus str. CCMP1375 were released, we incorporated them to GIB, and now you can search those data.
References (Institutes):
-Chlamydophila pneumoniae TW-183 (ALTANA Pharmaceuticals):
The genome sequence of Chlamydia pneumoniae TW183 and comparison with other Chlamydia strains based on whole genome sequence analysis,Unpublished.

-Haemophilus ducreyi 35000HP (Columbus Children's Research Institute): The Complete Genome Sequence of Haemophilus ducreyi,Unpublished.
-Prochlorococcus marinus subsp. marinus str. CCMP1375 (Genoscope and Station Biologique de Roscoff): Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a near minimal oxyphototrophic genome, Unpublished.
Services: ddbj Keywords:

PRF Rel. 92 was released

July 24,2003
PRF (Protein Research Foundation)/SEQ database Release 92 was released on Jul. 24, 2003 at DDBJ. PRF Release 92 consists of 233,109 entries, and the total number of residues reached 83,162,444.
Services: ddbj Keywords:

Updates of "Conference on information biology"

July 22,2003
Following conferences were added to "Conference on information biology".
Services: ddbj Keywords:

PIR rel. 77 was released

July 16,2003
PIR rel. 77 was released on Jul. 16, 3003 at DDBJ. PIR rel. 77 consists of 283,329 entries, and the total number of residues reached 96,175,589 aa.
Services: ddbj Keywords:

NIG Network service temporary down--Cancelled

July 14,2003
NIG (National Institute of Genetics) network service scheduled for today was cancelled.
NIG Network service, DDBJ network service, and NIG supercomputer (supernig and minerva) service are available as usual.
Services: ddbj Keywords:

NIG Network service temporary down

July 11,2003
NIG (National Institute of Genetics) network service will be stopped at the following schedule because of the the planned blackout of the Institute.
DDBJ network service and NIG supercomputer (supernig and minerva) service will also be unavailable.
Thank you very much for your understanding and cooperation.
Jul. 14(MON) 18:00 - Jul. 15(TUE)11:00
Services: ddbj Keywords:

NIG Network service temporary down

July 11,2003
NIG (National Institute of Genetics) network service will be unavailable at the following schedule because of the network maintenance.
DDBJ network service and NIG supercomputer (supernig and minerva) service will also be unavailable.
Thank you very much for your understanding and cooperation.
Jul. 13(SUN), 2003 13:00 - 18:00
Services: ddbj Keywords:

Update of DDBJ top page

July 10,2003
DDBJ top page was updated. "FTP site for DDBJ release" and some other links are added.
Services: ddbj Keywords:

URL change of SQmatch

July 09,2003
SQmatch is a database search service provided on the DDBJ web. It was developed by DDBJ for matching a regular expression against sequences in DDBJ and DAD databases, and is useful for the search of short length sequences and sequences which include "N".
The URL of SQmatch will be changed from July 15, 2003.
New URL is:
English http://sqmatch.ddbj.nig.ac.jp/top-e.html
Japanese http://sqmatch.ddbj.nig.ac.jp/top-j.html
Old URL will be stopped on August 15, 2003. So, please update your bookmarks and links. This change accompanies a change of the port number from current #8000 to new #80 (standard port).
Because of this change, troubles of accessing to SQmatch due to port number mismatch will be solved. Contents of the service has no change.
Thank you very much for your understanding and cooperation.
Services: ddbj Keywords:

Pirellula sp. strain 1 was added to GIB

July 04,2003
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.Because the genome sequence data of Pirellula sp. strain 1 was released, we incorporated it to GIB, and now you can search those data.
Institute: MPIMM
Reference: Complete genome sequence of the marine planctomycete Pirellula sp. strain 1, Proc. Natl. Acad. Sci. U.S.A. 100 (14), 8298-8303(2003)
Services: ddbj Keywords:

Update of "Links" for Information Biology

July 04,2003
Link to Other web pages on Information Biology was updated.A lot of web information including SNP and gene-expression are newly added.
Please visit.
Services: ddbj Keywords:

DAD rel. 24 was released

July 04,2003
DDBJ amino acid database (DAD) Release 24 was released on July 3rd, 2003 at DDBJ. DAD Release consists of 1,429,344 entries,and the total number of residues reached 441,769,888.
FTP site for DB download
Services: ddbj Keywords:

Helicobacter hepaticus ATCC 51449 was added to GIB

July 01,2003
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.Because the genome sequence data of Helicobacter hepaticus ATCC 51449 was released, we incorporated it to GIB, and now you can search those data.
Institute: MWG
Reference: The complete genome sequence of the carcinogenic bacterium Helicobacter hepaticus, Proc. Natl. Acad. Sci. U.S.A. 100 (13), 7901-7906 (2003)
Services: ddbj Keywords:

Statistics [Top 30 organisms according to the total number of nucleotides] Update

June 27,2003
Top 30 organisms according to the total number of nucleotides (- DDBJ rel.54) in DDBJ statistics was updated with
releasing DDBJ Rel. 54.
Macaca mulatta (rhesus monkey) ranked in 11th, it was 98th at previous release.Click the organism name to view the graph of change.
Services: ddbj Keywords:

DDBJ Rel. 54 Completed

June 23,2003
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public.We completed DDBJ Release 54 in June 23, 2003.DDBJ Release 54 consists of 25,149,821 entries, and the number of bases reached 32,162,041,177.
Services: ddbj Keywords:

DDBJ network services reopening

June 17,2003
We resumed [search and analysis, FTP] services.Thank you very much for your understanding and cooperation.
Services: ddbj Keywords:

DDBJ network services temporary down

June 16,2003
Following DDBJ network services are suspended temporarily because of the network trouble. Thank you very much for your understanding and cooperation.
[search and analysis , FTP]
Services: ddbj Keywords:

Supernig periodic maintenance

June 16,2003
Supernig service will be unavailable during the following date because of the periodic maintenance.
Thank you very much for your understanding and cooperation.
Jun. 20 (Fri) 12:00- 21:00
Services: ddbj Keywords:

Mycoplasma gallisepticum R was added to GIB

June 12,2003
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.Because the genome sequence data of Mycoplasma gallisepticum R was released, we incorporated it to GIB, and now you can search those data.
Institute: CEVR
Reference: The complete genome sequence of the avian pathogen Mycoplasma gallisepticum strain R, Microbiology (2003) In press
Services: ddbj Keywords:

Scheduled stop of the GIB server

June 10,2003
GIB server will be stopped for a machine maintenance.Thank you very much for your cooperation.
From Jun 14 (Sat) 5:00 pm to Jun 15 (Sun) 8:00 am
Services: ddbj Keywords:

PRF Rel. 91 was released

June 09,2003
PRF (Protein Research Foundation)/SEQ database Release 91 was released on Jun. 9th, 2003 at DDBJ. PRF Release 91 consists of 229,482 entries, and the total number of residues reached 81,951,321.
Services: ddbj Keywords:

Updates of "Conference on information biology"

June 04,2003
Following conference was added to "Conference on information biology".
Services: ddbj Keywords:

NIG Network service temporary down

May 27,2003
NIG (National Institute of Genetics) network service will be unavailable at the following schedule because of the network maintenance.
DDBJ network service and NIG supercomputer (supernig and minerva) service will also be unavailable.
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Jun. 3 (TUE), 2003 18:00 - 21:00
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New function was added to BLAST service

May 23,2003
BLAST is
aprogram for homology search.
DDBJ added new function for multiple query sequences to BLAST service. You can now ask multiple query sequences at once.
This function is only available when "E-mail" is selected as the way to get result. Please use it.
Example of multiple query sequence (multi FASTA format):    
>my query sequence 1    CACCCTCTCTTCACTGGAAAGGACACCATGAGCACGGAAAGCATGATCCAGG
ACGTGGAA    GCTGGCCGAGGAGGCGCTCCCCAGGAAGACAGCAGGGCCCCAGGGCTCCAGGCGGTGCTG    
GTTCCTCAGCCTCTTCTCCTTCCTGCTCGTGGCAGGCGCCGCCAC    
>my query sequence 2    GGCCAGGGCACCCAGTCTGAGAACAGCTGCACCCGCTTCCCAGGCAACCTG
CCTCACATG    CTTCGAGACCTCCGAGATGCCTTCAGCAGAGTGAAGACTTTCTTTCAAATGAAGGATCAG    
CTGGACAACATATTGTTAAAGGAGTCCTTGCTGGAGGACTTTAAG    
>my query sequence 3    ATGGGTCTCACCTCCCAACTGCTTCCCCCTCTGTTCTTCCTGCTAGCATGT
GCCGGCAAC    TTTGCCCACGGACACAACTGCCATATCGCCTTACGGGAGATCATCGAAACTCTGAACAGC    
CTCACAGAGCAGAAGACTCTGTGCACCAAGTTGACCATAACGGAC    
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SAKURA temporarily down

May 16,2003
In order to conduct the maintenance work, SAKURA will be stopped the following date. Thank you very much for your understanding and cooperation.
From 9:00 to 10:00 May 19(Mon)
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EPD Data mirrored at DDBJ

May 13,2003
To periodically update EPD(Eukaryotic Promotor Database) data which is included in the category of DDBJ homology search service , DDBJ opened a EPD mirror site . It is also linked from Anonymous FTP of the DDBJ and "Link to Other web pages on Information Biology" .
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PIR rel. 76 was released

May 09,2003
PIR rel. 76 was released on May 9, 3003 at DDBJ. PIR rel. 76 consists of 283,308 entries, and the total number of residues reached 96,168,669 aa.
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Minerva periodic maintenance

May 09,2003
Minerva service will be unavailable during the following date because of the periodic maintenance.
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May 16 (Fri) 12:00- 21:00
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Data were added to GIB

May 06,2003
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.Because the genome sequence data of Shigella flexneri 2a 2457T, Nitrosomonas europaea ATCC 19718, and Bacillus anthracis Ames were released, we incorporated them to GIB, and now you can search those data.
References(Institutes):
-Shigella flexneri 2a 2457T(University of Wisconsin):
Complete Genome Sequence of the Q-fever Pathogen, Coxiella burnetii, Proc. Natl. Acad. Sci. U.S.A. (2003) In press

-Nitrosomonas europaea ATCC 19718(JGI):
Complete genome sequence of the ammonia oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea, J. Bacteriol. 185(9), 2759-2773 (2003)

-Bacillus anthracis Ames(TIGR):
Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis, Science 296 (5575), 2028-2033 (2002)

Sequence and organization of pXO1, the large Bacillus anthracis plasmid harboring the anthrax toxin genes, J. Bacteriol. 181 (20), 6509-6515 (1999)
The Genome Sequence of Bacillus anthracis Ames and Comparison to Closely-Related Bacteria, Nature 423, 81-86 (2003)
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SINET network service temporary down

May 01,2003
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.
May 3 (SAT) 16:00 - 17:00
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PRF Rel. 90 was released

April 30,2003
PRF (Protein Research Foundation)/SEQ database Release 90 was released onApr. 30 at DDBJ. PRF Release 90 consists of 225,081 entries, and the totalnumber of residues reached 80,474,390.
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International Consortium Completes Human Genome Project

April 23,2003
Speeches and Statements by Prime Minister
English translation / Japanese
International Consortium Completes Human Genome Project
Joint Proclamation by the Heads of Government of Six countries Regarding the Completion of the Human Genome Sequence (EnglishJapanese translation
Sequences
Note:"DDBJ/CIB Human Genomics Studio" project, started in Apr. 2000, developed an original method of assembling the data of human genome sequence and producing contig, and created original chromosome sequence based on genome sequences which have been registered to the international DNA databases, DDBJ/EMBL/GenBank, and publicized from them. (last updated: May 8, 2002). Accordingly, at the present stage, "DDBJ/CIB Human Genomics Studio" offers draft sequence.Human genome (Build 35.1, "finished" sequences) download pageIn this page, contig list for each chromosome are disclosed. These list are based on "Build 35.1" which is the most recent (as of Aug. 2004) human build for which full annotation is available, released by NCBI, USA. Build 35.1 includes the finished human genome sequence determined by the International Human Genome Sequencing Consortium with the one determined by Celera.
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GIB maintenance stop

April 23,2003
GIB server will be stopped for a machine maintenance.
From April 26 (Sat) 5:00 pm to April 27 (Sun) 8:00 am
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S&W search service reopening

April 22,2003
We resumed S&W search service.Thank you very much for your understanding and cooperation.
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Submission for TPA and WGS

April 21,2003
DDBJ started to accept TPA (Third Party Annotation) and WGS (Whole Genome Shotgun) submission.Please refer here for more information.
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S&W search service temporary down

April 21,2003
S&W search service is suspended temporarily because of the server trouble. The service will be resumed in a few days. Thank you very much for yourunderstanding and cooperation.
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SWISS-PROT Rel. 41 was released

April 21,2003
SWISS-PROT Rel. 41 was released on Apr. 21, 2003 at DDBJ.SWISS-PROT Rel. 41 consists of 122,564 entries,and the total number of residues reached 44,986,459.
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Data were added to GIB

April 21,2003
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete microbial genome sequences. Because the genome sequence data of
Coxiella burnetii RSA 493,Streptomyces avermitilis MA-4680,Chlamydophila caviae GPIC and Bacillus cereus ATCC 14579 were released, we incorporated them to GIB, and now you can search those data.
- References(Institutes):
- Coxiella burnetii RSA 493(TIGR):
Complete Genome Sequence of the Q-fever Pathogen, Coxiella burnetii, Proc. Natl. Acad. Sci. U.S.A. (2003) In press

- Streptomyces avermitilis MA-4680(Kitasato University, NITE):
Complete Genome Sequence and Comparative Analysis of the Industrial Microorganism Streptomyces avermitilis, Nat. Biotechnol. (2003) In press

   Genome sequence of an industrial microorganism Streptomyces avermitilis: Deducing the ability of producing secondary metabolites, Proc. Natl. Acad. Sci. U.S.A. 98, 12215-12220 (2001)
- Chlamydophila caviae GPIC(TIGR):
Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae, Nucleic Acids Res. 31 (8), 2134-2147 (2003)

- Bacillus cereus ATCC 14579(Integrated Genomics Inc.):
Genome sequence of Bacillus cereus ATCC 14579 and comparison with Bacillus anthracis, Nature (2003) In press

   The number of ribosomal RNA operons in Bacillus cereus, Unpublished
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Human genome (Build 32, "finished" sequences) download page was released

April 18,2003
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Updates of "Conference on information biology"

April 15,2003
Following conferences were added to "Conference on information biology".
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SAKURA server temporarily down

April 14,2003
SAKURA service will be unavailable during the following date because ofthe maintenance. Thank you very much for your understanding and cooperation.
Apr. 20 (SUN) 22:00-23:00 (Japanese Standard Time)
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DAD rel. 23 was released

April 04,2003
DDBJ amino acid database (DAD) Release 23 was released on Apr. 4th, 2003 at DDBJ. DAD Release 23 consists of 1,324,437 entries,and the total number of residues reached 410,343,359.
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Supernig periodic maintenance

April 03,2003
Supernig service will be unavailable during the following date because of the periodic maintenance.
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Apr. 10 (Thu) 10:00- 18:00
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Data were added to GIB

April 03,2003
GIB (Genome Information Broker forMicrobial Genomes) provides a comprehensive view of the complete microbial genome sequences.Because the genome sequence data of Bacteroides thetaiotaomicron VPI-5482 and Enterococcus faecalis V583 were released, we incorporated them to GIB, and now you can search those data.
Bacteroides thetaiotaomicron VPI-5482(by Washington University School of Medicine): A Genomic View of the Human-Bacteroides thetaiotaomicron Symbiosis,Science 299 (5615), 2074-2076 (2003)
Enterococcus faecalis V583(by TIGR): Role of Mobile DNA in the Evolution of Vancomycin-Resistant Enterococcus faecalis, Science 299 (5615), 2071-2074 (2003)
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Salmonella enterica subsp. enterica serovar Typhi Ty2 was added to GIB

March 27,2003
GIB (Genome Information Broker forMicrobial Genomes) provides a comprehensive view of the complete microbialgenome sequences.Because the genome sequence data of Salmonella enterica subsp. enterica serovar Typhi Ty2 was released,we incorporated it to GIB, and now you can search those data.
Institute: University of Wisconsin
Reference: Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18, J. Bacteriol. 185 (7), 2330-2337 (2003)
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NIG Network service temporary down

March 27,2003
NIG (National Institute of Genetics) network service will be unavailable at the following schedule because of the network maintenance.
DDBJ network service and NIG supercomputer (supernig and minerva) service will also be unavailable.
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Apr. 2(WED), 2003 18:00 - 20:00
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DDBJ Rel. 53 Completed

March 24,2003
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public.We completed DDBJ Release 53 in March 24, 2003.DDBJ Release 53 consists of 23,250,813 entries, and the number of bases reached 29,711,299,332.
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GIB display was changed

March 17,2003
GIB (Genome Information Broker forMicrobial Genomes) provides a comprehensive view of the complete microbialgenome sequences.DDBJ changed display of the top page. Main points of this change are as
follows:
  • Because more than 100 genome informations are provided, rough taxonomy levels could be selected at the GIB top page
  • Categories of genes functions could be shown at chromosome maps of each genomes.
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FTP download site was opened

March 14,2003
FTP download site of DDBJ can be used for download of DDBJ periodical release and daily updated data. But present site is incovenient for users. DDBJ newly added FTP download site (Anonymous FTP of the DDBJ) in DDBJ web pages. In this site, file size of data are reduced so that downloading can be made easily.
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Recovery of the DDBJ web pages

March 13,2003
Due to an accident of the WWW server, DDBJ web pages other than SAKURA and search and analyses service pages could not be accessed from the morning to 6 pm on March 12. They were recovered on the same
day and now you can access all pages as usual.
We apologize for your inconvenience and appreciate for your understanding.
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Pseudomonas syringae pv. tomato str. DC3000 was added to GIB

March 11,2003
GIB (Genome Information Broker forMicrobial Genomes) provides a comprehensive view of the complete microbial genome sequences.Because the genome sequence data of Pseudomonas syringae pv. tomato str.DC3000 was released,we incorporated it to GIB, and now you can search those data.
Institute: Cornell University
Reference: Complete Sequence of Pseudomonas syringae,Unpublished
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Over three billion bases released !

March 07,2003
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 three billion on Mar. 7.
- As of Mar. 7, 2003
The total number of released bases 30,019,841,567 (23,259,781 entries)
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Data were added to GIB

March 06,2003
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 SSI-1 and Vibrio parahaemolyticus O3:K6 RIMD 2210633 were released, we incorporated it to GIB, and now you can search those data.
References (Institutes):
Streptococcus pyogenes SSI-1 (GIRC): The genome of invasive Streptococcus pyogenes; a comparative analysis of S. pyogenes SSI-1, SF370 and MGAS8232., Unpublished (2002)
Vibrio parahaemolyticus O3:K6 RIMD 2210633 (GIRC):
A filamentous phage associated with recent pandemic Vibrio parahaemolyticus O3:K6 strains, J. Clin. Microbiol. 38, 2156-2161 (2000)
Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V cholerae, Lancet 361, 743-749 (2003)
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Scheduled stop of the GIB server

March 04,2003
GIB server will be stopped for a version-up
     from: March 14 (Fri) 5:00 pm
     to: March 17 (Mon) 8:00 am
Thank you very much for your cooperation.
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Data were added to GIB

February 27,2003
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Lactobacillus plantarum WCFS1, Tropheryma whipplei TW08/27 and Tropheryma whipplei str. Twist were released, we incorporated it to GIB, and now you can search those data.
References (Institutes):
Lactobacillus plantarum WCFS1 (WCFS): Complete genome sequence of Lactobacillus plantarum WCFS1, Online Publication.
Tropheryma whipplei TW08/27 (The Sanger Centre): Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei, Lancet 361, 627-634(2003).
Tropheryma whipplei str. Twist (Universite de la Mediterranee): Tropheryma whipplei illustrates the diversity of gene loss patterns in small genome bacterial pathogens, Unpublished
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Updates of "Conference on information biology"

February 19,2003
Following conferences were added to "Conference on information biology".
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Xylella fastidiosa Temecula1 and Clostridium tetani Massachusetts E88 were added to GIB

February 12,2003
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Xylella fastidiosa Temecula1 and Clostridium tetani Massachusetts E88 were released, we incorporated it to GIB, and now you can search those data.
Xylella fastidiosa Temecula1
Institute: AEG Brazilian Consortium
Reference: Comparative Analyses of the Complete Genome Sequences of Pierce's Disease and Citrus Variegated Chlorosis Strains of Xylella fastidiosa,J. Bacteriol. 185 (3), 1018-1026 (2003)
Clostridium tetani Massachusetts E88
Institute: Goettingen Genomics Laboratory
Reference: The genome sequence of Clostridium tetani, the causative agent of tetanus disease, Proc. Natl. Acad. Sci. U.S.A. 100 (3) (2003) In press
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NIG Network service temporary down

February 10,2003
NIG (National Institute of Genetics) network service will be unavailable at the following schedule because of the network maintenance.
DDBJ network service and NIG supercomputer (supernig and minerva) service will also be unavailable.
Thank you very much for your understanding and cooperation.
Feb. 17(MON), 2003 18:00 - 20:00
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Updates of "Conference on information biology"

February 05,2003
Following conferences were added to "Conference on information biology".
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PRF Rel. 89 was released

January 30,2003
PRF (Protein Research Foundation)/SEQ database Release 89 was released on Jan. 29 at DDBJ. PRF Release 89 consists of 216,752 entries, and the total number of residues reached 77,655,726.
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Buchnera aphidicola (Baizongia pistaciae) was added to GIB

January 29,2003
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 (Baizongia pistaciae) was released, we incorporated it to GIB, and now you can search those data.
Institute: CNB
Reference: Reductive genome evolution in Buchnera aphidicola, Proc. Natl. Acad. Sci. U.S.A. 100 (2), 581-586 (2003)
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PIR rel. 75 was released

January 24,2003
PIR rel. 75 was released on Jan. 24, 3003 at DDBJ.PIR rel. 75 consists of 283,268 entries, and the total number of residues reached 96,152,078 aa.
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DAD rel. 22 was released

January 20,2003
DDBJ amino acid database (DAD) Release 22 was released on Jan. 20, 2003 at DDBJ. DAD Release 22 consists of 1,218,918 entries, and the total number of residues reached 376,251,148.
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Supernig periodic maintenance

January 10,2003
Supernig service will be unavailable during the following date because of the periodic maintenance.
Thank you very much for your understanding and cooperation.
Jan. 17(Fri) 10:00-21:00
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NIG Network service temporary down

January 10,2003
NIG (National Institute of Genetics) network service will be unavailable at the following schedule because of the network maintenance.
DDBJ network service and NIG supercomputer (supernig and minerva) service will also be unavailable.
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Jan. 15(WED), 2003 18:00 - 19:00
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Staphylococcus epidermidis ATCC 12228 was added to GIB

January 06,2003
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of Staphylococcus epidermidis ATCC 12228 was released, we incorporated it to GIB, and now you can search those data.
Institute: Chinese National Human Genome Center at Shanghai
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Staphylococcus epidermidis ATCC 12228

January 06,2003
GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences. Because the genome sequence data of
Staphylococcus epidermidis ATCC 12228 was released, we incorporated it to GIB, and now you can search those data.
Institute: Chinese National Human Genome Center at Shanghai
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