DNA Data Bank of Japan

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Genome data was added to GIB Dec. 27, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Synechococcus elongatus PCC 6301 was released by Nagoya University, we incorporated it to GIB, and now you can search those data.
Reference: Complete genome structure of the unicellular cyanobacterium Anacystis nidulans 6301 (Synechococcus sp. PCC6301), Unpublished (2004)
 
DDBJ Rel. 60 Completed Dec. 24, 2004
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public. We completed DDBJ Release 64 in Dec. 24, 2004. DDBJ Release 60 consists of 40,583,945 entries, and the number of bases reached 44,416,752,273.
FTP site for periodical release and new data download
 
PRF Rel. 100 was released Dec. 22, 2004
PRF (Protein Research Foundation)/SEQ database Release 100 was released on Dec. 22, 2004 at DDBJ. PRF Release 100 consists of 291,515 entries, and the total number of residues reached 102,321,978.
 
Data were added to GIB Dec. 20, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Zymomonas mobilis subsp. mobilis ZM4, Francisella tularensis subsp. tularensis and Silicibacter pomeroyi DSS-3 were released by Macrogen, Inc., Uppsala University and TIGR, we incorporated them to GIB, and now you can search those data.
Reference:
Zymomonas mobilis subsp. mobilis ZM4: The genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4, Nat Biotechnol. 2004 Dec 12; [Epub ahead of print]
Francisella tularensis subsp. tularensis: Complete genome sequence of Francisella tularensis (SCHU S4) the causative agent of tularemia, Unpublished.
Silicibacter pomeroyi DSS-3: Genome Sequence of Silicibacter pomeroyi Reveals Unique Adaptations to the Marine Environment, Nature 432, 910-913 (2004)
 
Data were added to GIB Dec. 15, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Anaplasma marginale str. St. Maries, Salmonella enterica subsp. enterica serovar Paratypi A ATCC 9150 and Geobacillus kaustophilus HTA426 were released by Washington State University, Washington University and JAMSTEC, we incorporated them to GIB, and now you can search those data.
References:
Anaplasma marginale str. St. Maries: Complete genome sequencing of Anaplasma marginale reveals that the surface is skewed to two superfamilies of outer membrane proteins, Proc. Natl. Acad. Sci. U.S.A. (2005) In press
Geobacillus kaustophilus HTA426: Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus, Nucleic Acids Res. 32, 6292-6303 (2004)
 
Data were added to GIB Dec. 9, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Azoarcus sp. EbN1 and Idiomarina loihiensis L2TR were released by Max Planck Institute and University of Hawaii, we incorporated them to GIB, and now you can search those data.
References:
Azoarcus sp. EbN1:
Genes involved in the anaerobic degradation of ethylbenzene in a denitrifying bacterium, strain EbN1, Arch. Microbiol. 178(6), 506-516(2002).
The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1, (er) Archives of Microbiology DOI, 10.1007/s00203-004-0742-9.
 
Suspension of the DDBJ activity during the New Year Holidays Dec. 7, 2004
We at DDBJ will suspend our business for receiving and releasing data during the New Year Holidays from December 29th, 2004 to January 3rd, 2005.
We will resume the normal business on January 4th, 2005. Please note in particular that SAKURA will stop in operation from December 27th, 2004 to January 4th, 2005 and the new daily update will not be released in the period from December 27th, 2004 to January 4th, 2005.
Thank you very much for your understanding and cooperation.
We wish you a Merry Christmas and Happy New Year.
 
"getentry" (web version) version number searches, E-mail Search Server get-version, amd SQmatch services stopped Dec. 6, 2004
"getentry" (web version) version number searches, E-mail Search Server get-version, amd SQmatch services has stopped because of a system trouble. We would appreciate your understanding and cooperation. Resumption will be annouced at DDBJ web siste soon after recovery of the systems.
-->Services are resumed at 16:00. Thank you for your cooperation.
 
Genome data was added to GIB Dec. 3rd, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Bacillus clausii KSM-K16 was released by Kao Corporation, we incorporated it to GIB, and now you can search those data.
Reference:
- High-resolution crystal structure of M-protease: phylogeny aided analysis of the high-alkaline adaptation mechanism, Protein Eng. 10, 627-634 (1997)
- Molecular cloning and nucleotide sequence of the gene for an alkaline protease from the alkalophilic Bacillus sp. KSM-K16, J. Ferment. Bioeng. 78, 105-108 (1994)
- Purification and properties of an alkaline protease from alkalophilic Bacillus sp. KSM-K16, Appl. Microbiol. Biotechnol. 43, 473-481 (1995)
- The complete genome sequence of the alkaliphilic Bacillus clausii KSM-K16, Unpublished (2003)
 
Genome data was added to GIB Nov. 25, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Thermus thermophilus HB8 was released by NAIST, we incorporated it to GIB, and now you can search those data.
Reference: Complete genome sequence of Thermus thermophilus HB8, Unpublished (2004)
 
Data were added to GIB Nov. 22, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Streptococcus thermophilus LMG 18311 and Streptococcus thermophilus CNRZ1066 were released by Institut National de la Recherche Agronomique, we incorporated them to GIB, and now you can search those data.
References: Complete genome sequence and comparative analysis of the dairy bacterium Streptococcus thermophilus, (er) Nat. Biotechnol. (2004)
 
Updates of "Conference on information biology" Nov. 22, 2004
Following conference was added to "Conference on information biology".
 
Updates of "Conference on information biology" Nov. 19, 2004
Following conferences were added to "Conference on information biology".
 
Great increase of Mus musculus molossinus nucleotide sequence data Nov. 9, 2004
Total number of the mouse nucleotides (Mus musculus molossinus) greatly increased from 44,452 bp to 279,762,931 bp in the latest DDBJ release (DDBJ Rel. 59).
[DDBJ statistics / Top 30 organisms according to the total number of nucleotides (-DDBJ rel.59)]
This big growth is caused by the addition of 337,471 entries' nucleotides released by RIKEN Genomic Sciences Center (RIKEN GSC) in 2004 June into 44,452 bp Mus musculus molossinus nucleotides released so far. Sequences of these nucleotides are Mus musculus molossinus-MSM mouse BAC clone library end sequences prepared by Dr. Kuniya Abe, RIKEN BioResource Center (RIKEN BRC).
Detailed data will be described in the following paper.
Abe K., Noguchi H., Tagawa K., Yuzuriha M., Toyoda A., Kojima T., Ezawa K., Saitou N., Hattori M., Sakaki Y., Moriwaki K., and Shiroishi T. (2004) ontribution of Asian mouse subspecies Mus musculus molossinus to genomic constitution of strain C57BL/6J, as defined by BAC end sequence-SNP analysis. Genome Research (in press).
Accession numbers are AG275743-AG613213. The sequences are available from DDBJ 's getentry. MSM BAC clones are available from "RIKEN BioResource Center DNA BANK" where clones are deposited. For details, please see MSM Mouse BAC clones & Library.
 
NIG Network service temporary down Nov. 5th, 2004
NIG (National Institute of Genetics) network service will be unavailable at the following schedule because of the electric power cut. DDBJ network service and NIG supercomputer (supernig and minerva) service will also be unavailable. Thank you very much for your understanding and cooperation.
From Nov.12(FRI) 17:00 to Nov.13(SAT) 22:00
* SAKURA system will be unavailable at the following schedule.
  From Nov.12(FRI) 15:00 to Nov.15(MON) 9:00 (JST)
 
Finished Human Genome Sequence was published Nov. 5th, 2004
The International Human Genome Sequencing Consortium(IHGSC) published the finished human genome sequence in Nature (vol.431, pp. 931 - 945 ; Oct. 21, 2004)　
In February 2001, the IHGSC had reported a draft sequence, and proclaimed the completion of essential sequencing in April, 2003. In the latest issue appeared in Nature, it covers more than 99% of the euchromatic portion of the human genome.
The finished human genome sequence can be accessed at the following DDBJ web site.
Human genome (Build 35.1, "finished" sequences) download page
Please see also the following hitsorial traces.
  - DDBJ/CIB Human Genomics Studio（draft sequence）
  - International Consortium Completes Human Genome Project
 
Genome data was added to GIB Nov. 5th, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Haloarcula marismortui ATCC 43049 was released by Institute for Systems Biology, we incorporated it to GIB, and now you can search those data.
Reference: Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea., Genome Res. 2004 Nov;14(11):2221-34.
 
CON entries revision due to the removal of sequence length limitation Oct. 28. 2004
Since INSD (the International Nucleotide Sequence Databases) had a rule to limit the sequence length for 1 entry to less than 350 kbp, DDBJ divided some long sequences during the process of their submission. Such divided sequences were assigned the accession numbers respectively, and were registered as piece entries. To inform this existence of piece entries, we made a CON(Contig/Constructed) entry, and released the information for the construction joined piece entries.
In June 2004, INSD removed the limitation of sequence length. In accordance with this removal, DDBJ plans to revise such divided sequences into a single entry for consolidation of the information.
DDBJ revises CON and piece entries as follows;
  • The accession number assigned to CON entry would be remained in the revised entry.
  • Piece entries would be suppressed and their accession numbers would be kept as the secondary accession numbers* in the revised entry.
  • Sequences and features described in piece entries would be taken over to the revised entry.
  • The revised entry would be transferred from CON to the corresponding taxonomic division.
* Even after these revisions, when you use our retrieval tools such as getentry, you can get the revised entry by the search with accession numbers of both CON and piece entries.
Please see the following site about CON entry in detail.
http://www.ddbj.nig.ac.jp/sub/locus-e.html
 
Statistics [Top 30 organisms according to the total number of nucleotides] Update Oct. 25, 2004
Top 30 organisms according to the total number of nucleotides (- DDBJ rel.59) in DDBJ statistics was updated with releasing DDBJ Rel. 59. Mus musculus molossinus (a species of mouse) ranked in 21th, it was 3131th at previous release. Click the organism name to view the graph of change.
 
Amendment of SEGMENT entries Oct. 22, 2004
Before July 2004, DDBJ/EMBL/GenBank had assigned an accession number for each of sequences separated by unsequenced regions, and treated the entries of the sequences as SEGMENT entries.
However, as a result of the change of our annotation policy for such sequences, from July, 2004 we began to accept one sequence in which unsequenced regions are indicated as strings of "n"s. In the case that the length of an unsequenced region can be estimated, "n"s of the estimated length are inserted. In the case that the length of an unsequenced region is unknown, 100 "n"s are inserted.
At the same time, we are amending all of the SEGMENT entries submitted before July 2004 to combine them into a single entry in accordance with the above rules. Accession numbers of combined SEGMENT entries will be displayed as secondary accession numbers in a single entry. As for already published SEGMENT entries, we will re-release them after the amendment.
　
Example:
  Before: D85375   D85376
  After: D85376
We appreciate your understanding and cooperation.
If you have any questions and concerns about this matter, please send e-mail to us at ddbjupdt@ddbj.nig.ac.jp.
* If you wish to submit your sequence with unsequenced regions of unknown length via SAKURA, please select "multi-exons with unknown gaps" in "Categories" at "Hold-date information" page, and submit only sequenced regions. One sequence with strings of 100 "n"s in the unsequenced regions will be sent to DDBJ.
 
Data were added to GIB Oct. 21, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Legionella pneumophila Paris, and Legionella pneumophila Lens were released by Institut Pasteur, we incorporated them to GIB, and now you can search those data.
Reference:
Evidence in the Legionella pneumophila genome for exploitation of host cell functions and high genome plasticity, Nat. Genet. Oct 03 (2004) [Epub ahead of print]
 
Updates of "Conference on information biology" Oct. 21, 2004
Following conferences was added to "Conference on information biology".
 
Updates of "Conference on information biology" Oct. 20, 2004
Following conferences were added to "Conference on information biology".
 
PRF Rel. 99 was released Oct. 15, 2004
PRF (Protein Research Foundation)/SEQ database Release 99 was released on Oct. 15, 2004 at DDBJ. PRF Release 99 consists of 270,439 entries, and the total number of residues reached 95,682,341.
 
getentry [Version Number] search service temporary down Oct. 13, 2004
Getentry is the data retrieval system provided by DDBJ through web and E-mail.
[Version Number] search, a part of getentry service function, will be unavailable at the following schedule because of the server maintenance. Thank you very much for your understanding and cooperation
- Date: Oct. 20(WED) 10:00-13:00
- web : [Version Number] could not be selected
- get-version E-mail server (get-version@nig.ac.jp) will be unavailable
 
DAD rel. 29 was released Oct. 13, 2004
DDBJ amino acid database (DAD) Release 29 was released on Oct. 13, 2004 at DDBJ. DAD Release consists of 1,990,271 entries, and the total number of residues reached 612,044,833.
FTP site for DB download
 
Genome data were added to GIB Oct. 13, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Methylococcus capsulatus str. Bath and Mycoplasma hyopneumoniae 232 were released, we incorporated them to GIB, and now you can search those data.
Reference:
Methylococcus capsulatus str. Bath (The Institute for Genomic Research) : Genomic Insights into Methanotrophy: The Complete Genome Sequence of Methylococcus capsulatus (Bath), PLoS Biol. 2, 1616-1628 (2004)
Mycoplasma hyopneumoniae 232 (Iowa State University) : The genome sequence of Mycoplasma hyopneumoniae strain 232, the agent of swine mycoplasmosis, J. Bacteriol. (2004) In press
 
Genome data was added to GIB Oct. 4, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Bacteroides fragilis YCH46 was released by Kitasato Institute for Life Sciences, we incorporated it to GIB, and now you can search those data.
Reference: Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation., Proc. Natl. Acad. Sci. U.S.A. (2004) In press
 
Genome data were added to GIB Oct. 1st, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Burkholderia pseudomallei K96243 and Bacillus licheniformis DSM 13 were released, we incorporated them to GIB, and now you can search those data.
Reference:
Burkholderia pseudomallei K96243 (Sanger Institute): Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei, Proc. Natl. Acad. Sci. U.S.A. 101 (39), 14240-14245
Bacillus licheniformis DSM 13 (Goettingen Genomics Laboratory): The complete genome sequence of Bacillus licheniformis DSM13, an organism with great industrial potential, J. Mol. Microbiol Biotechnol, 7(4), 204-211 (2004)
 
DDBJ Rel. 59 Completed Sep. 30, 2004
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public. We completed DDBJ Release 59 in Sep. 30, 2004. DDBJ Release 59 consists of 37,926,117 entries, and the number of bases reached 42,245,956,937.
FTP site for periodical release and new data download
 
Genome data were added to GIB Sep. 27, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Mannheimia succiniciproducens MBEL55E and Legionella pneumophila subsp. pneumophila Philadelphia 1 were released, we incorporated them to GIB, and now you can search those data.
Reference:
Mannheimia succiniciproducens MBEL55E (Joint Genome Institute): The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens, Nat. Biotechnol. Sep 19 (2004)
Legionella pneumophila subsp. pneumophila Philadelphia 1 (Columbia University): The Genomic Sequence of the Accidental Pathogen Legionella pneumophila, Science 305 (5692), 1966-1968 (2004)
 
Genome data was added to GIB Sep. 24, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Burkholderia mallei ATCC 23344 was released by TIGR, we incorporated it to GIB, and now you can search those data.
Reference: Structural flexibility in the Burkholderia mallei genome, Proc. Natl. Acad. Sci. U.S.A. 101 (39), 14247-14251 (2004)
 
Genome data were added to GIB Sep. 17, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Bacillus cereus ZK and Bacillus licheniformis ATCC 14580 were released, we incorporated them to GIB, and now you can search those data.
Reference:
Bacillus cereus ZK (Joint Genome Institute): Complete genome sequence of Bacillus cereus ZK, Unpublished.
Bacillus licheniformis ATCC 14580 (Novozymes Biotech Inc.): Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species, Genome Biol. 5, R77 (2004)
 
Supernig periodic maintenance Sep. 13, 2004
Supernig service will be unavailable during the following date because of the periodic maintenance. Thank you very much for your understanding and cooperation.
Sep. 17th(FRI) from 12:00 to 21:00
 
NIG Network service temporary down Sep. 9, 2004
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.
Sep. 15th(Wed) from 12:00 to 13:00
 
Genome data was added to GIB Sep. 2nd, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Symbiobacterium thermophilum IAM1486 was released by Kitasato Institute for Life Sciences, we incorporated it to GIB, and now you can search those data.
Reference: Complete genome sequence of an uncultured bacterium Symbiobacterium thermophilum, Unpublished (2004)
 
Genome data were added to GIB Aug. 30, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Borrelia garinii PBi and Yersinia pseudotuberculosis IP32953 were released, we incorporated them to GIB, and now you can search those data.
Reference:
Borrelia garinii PBi (Institute of Molecular Biotechnology, Beutenbergstr): Comparative analysis of the Borrelia garinii genome, Unpublished.
Yersinia pseudotuberculosis IP32953 (Oak Ridge National Laboratory): Insights into the genome evolution of Yersinia pestis through whole genome comparison with Yersinia pseudotuberculosis, Unpublished.
 
Genome data was added to GIB Aug. 23, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Rickettsia typhi wilmington was released by Human Genome Sequencing Center, we incorporated it to GIB, and now you can search those data.
Reference: Complete Genome Sequence of Rickettsia typhi and Comparison with Sequences of Other Rickettsiae, J. Bacteriol. 186 (17), 5842-5855 (2004)
 
Genome data was added to GIB Aug. 20, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Desulfotalea psychrophila LSv54 was released by e.gene Biotechnologie GmbH, we incorporated it to GIB, and now you can search those data.
Reference: The genome of Desulfotalea psychrophila, a sulphate-reducing bacterium from permanently cold Arctic sediments. Environ Microbiol. 2004 Sep 6(9) 887-902
 
PRF rel. 98 was released Aug. 19, 2004
PRF (Protein Research Foundation)/SEQ database Release 98 was released on Aug. 18, 2004 at DDBJ. PRF Release 98 consists of 262,644 entries, and the total number of residues reached 93,074,728.
 
SWISS-PROT Rel. 44 was released Aug. 11, 2004
SWISS-PROT Rel. 44 was released on Aug. 11, 2004 at DDBJ. SWISS-PROT Rel. 44 consists of 153,871 entries, and the total number of residues reached 56,608,159.
FTP site for periodical release and new data download
 
Genome data was added to GIB Aug. 6th, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Leifsonia xyli subsp. xyli CTCB07 was released by University of Campinas, we incorporated it to GIB, and now you can search those data.
Reference: The genome sequence of the Gram-positive sugarcane pathogen Leifsonia xyli subsp. xyli, Mol. Plant Microbe Interact. 17 (8), 827-836 (2004)
 
Genome data was added to GIB Aug. 5th, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Streptococcus pyogenes MGAS10394 was released by NIH, we incorporated it to GIB, and now you can search those data.
Reference: Progress toward Characterization of the Group A Streptococcus Metagenome: Complete Genome Sequence of a Macrolide-Resistant Serotype M6 Strain, J. Infect. Dis. 190 (4), 727-738 (2004)
 
Genome data was added to GIB Aug. 3rd, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Propionibacterium acnes KPA171202 was released by Goettingen Genomics Laboratory, we incorporated it to GIB, and now you can search those data.
 
Supernig service reopening Jul. 29, 2004
We resumed supernig service on 7pm, Jul.28. Thank you very much for your understanding and cooperation.
 
Supernig service temporary down Jul. 28, 2004
Supernig service is suspended temporarily because of the system trouble. After the restoration, we will announce it here. We apologize for the inconvenience and thank you for your understanding.
 
S&W SEARCH service reopening Jul. 27, 2004
We resumed S&W SEARCH service on Jul. 26. The request received between system troubles is performed in order. Thank you very much for your understanding and cooperation.
 
Statistics [Top 30 organisms according to the total number of nucleotides] Update Jul. 26, 2004
Top 30 organisms according to the total number of nucleotides (- DDBJ rel.58) in DDBJ statistics was updated in accordance with release of DDBJ Rel. 58. Click the organism name to view the graph of change.
 
Genome data was added to GIB Jul. 22, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Mesoplasma florum L1 was released by MIT, we incorporated it to GIB, and now you can search those data.
 
The modification of file names for WGS data on the FTP site Jul. 16, 2004
DDBJ/EMBL/GenBank are collecting and maintaining the sequences from the proceeding genome projects as WGS database. DDBJ provides the data on the page, Anonymous FTP of the DDBJ, at the site, WGS data.
Up to now, DDBJ named WGS data files at the FTP site after their organism names. However, since the number of WGS projects is significantly increasing, it is inconvenient to maintain the correspondence between files and projects. From now on, DDBJ has modified the naming convention and has renamed the WGS data files after the prefixes of their accession numbers. You can see the organism name corresponding to each file in the summary table. It will start from 14:00 on Jul. 20.
 
SWISS-PROT Rel. 43 was released Jul. 16, 2004
SWISS-PROT Rel. 43 was released on Jul. 16, 2004 at DDBJ. SWISS-PROT Rel. 43 consists of 146,720 entries, and the total number of residues reached 54,093,154.
FTP site for periodical release and new data download
 
Inconsistency of some entries of DDBJ Release 58 Jul. 15, 2004
Inconsistency was found in some entries of the latest DDBJ Release 58 (released on June 30, 2004).
Nature of inconsistency: Description of "BASE COUNT" line was not included in some data.
Measures implemented: Defected data were corrected, and released again on July 9.
List of corrected files:
We DDBJ regret our mistake.
[Note on "BASE COUNT" line]
Although GenBank had dropped the BASE COUNT line from their flat file format from GenBank Release 138 (Oct. 2003), we DDBJ still keep the BASE COUNT line in DDBJ flat file format, because we believe that this information is useful, such as computing the GC contents.
 
The tblastx program was added to BLAST Jul. 15, 2004
The tblastx program was added to DDBJ BLAST homology search services provided through web and E-mail. The tblastx program "Compares your nucleotide sequence with nucleotide sequence database by translating both sequences taking into account all six possible open reading frames". Because of this addition, from July 15, 2004, usable BLAST programs became 5 (new tblastx and present 4 types: blastn, blastp, blastx, tblastn)
 
Genome data were added to GIB Jul. 13, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the following two genome sequence data were released, we incorporated it to GIB, and now you can search those data.
Erwinia carotovora subsp. atroseptica SCRI1043 (Sanger Institute):
The genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica SCRI1043 and functional genomic identification of novel virulence factors, Unpublished.
Acinetobacter sp. ADP1 (Genoscope):
Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium, Unpublished.
 
Updates of "Conference on information biology" Jul. 8, 2004
Following conferences were added to "Conference on information biology".
 
Updates of "Conference on information biology" Jul. 5, 2004
Following conferences was added to "Conference on information biology".
 
Genome data was added to GIB Jul. 2nd, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the following two genome sequence data were released, we incorporated it to GIB, and now you can search those data.
Bacillus thuringiensis serovar konkukian str. 97-27 (Joint Genome Institute):
Complete genome sequence of Bacillus thuringiensis 97-27, Unpublished
Bacillus anthracis str. Sterne (Joint Genome Institute):
Complete genome sequence of Bacillus anthracis Sterne, Unpublished
 
Genome data was added to GIB Jul. 1st, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the following four genome sequence data were released, we incorporated it to GIB, and now you can search those data.
Staphylococcus aureus subsp. aureus MRSA252 (The Sanger Institute):
Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance, Proc. Natl. Acad. Sci. U.S.A. 101(26), 9786-9791(2004).
Staphylococcus aureus subsp. aureus MSSA476 (The Sanger Institute):
Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance, Proc. Natl. Acad. Sci. U.S.A. 101(26), 9786-9791(2004)
Bartonella henselae Houston-1 (Uppsala University):
The louse-borne human pathogen Bartonella quintana is a genomic derivative of the zoonotic agent Bartonella henselae, Proc. Natl. Acad. Sci. U.S.A. 101, 9716-9721 (2004)
Bartonella quintana Toulouse (Uppsala Universit):
The louse-borne human pathogen Bartonella quintana is a genomic derivative of the zoonotic agent Bartonella henselae, Proc. Natl. Acad. Sci. U.S.A. 101, 9716-9721 (2004)
 
DDBJ Rel. 58 Completed Jun. 30, 2004
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public. We completed DDBJ Release 58 in Jun. 30, 2004. DDBJ Release 58 consists of 34,917,581 entries, and the number of bases reached 39,812,635,108.
FTP site for periodical release and new data download
 
NIG Network service temporary down Jun. 28, 2004
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. 5th(MON) from 18:00 to 22:00
 
Scheduled stop of SAKURA system Jun. 23, 2004
In order to conduct the maintenance work, SAKURA system will be stopped the following date:
From 18:00 to 20:00 Jun 28(Mon) (Japanese Standard Time)
We would appreciate your understanding and cooperation in advance.
 
DDBJ HP was renewed Jun. 21, 2004
As you were already aware, DDBJ HP was renewed in its design and function. For example, at each pages, SRS service was added to search function. There are some pages where URL was changed. So, please change your bookmarks if necessary. We hope you can use our DDBJ HP more conveniently than ever.
 
S&W SEARCH service temporary down Jun. 21, 2004
S&W SEARCH service is suspended temporarily because of the system trouble. Your request will be queued and the result will be returned after the maintenance. Thank you very much for your understanding and cooperation.
 
Genome data was added to GIB Jun. 16, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Corynebacterium glutamicum ATCC 13032 (U.Bielefeld) was released, we incorporated it to GIB, and now you can search those data.
Institute: University Bielefeld
Reference: The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins, J. Biotechnol. 104(1-3), 5-25(2003).
 
Minerva periodic maintenance Jun. 14, 2004
Minerva service will be unavailable during the following date because of the periodic maintenance. Thank you very much for your understanding and cooperation.
Jun. 18 (Fri) 12:00- 21:00
 
Genome data was added to GIB Jun. 11, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Picrophilus torridus DSM 9790 was released, we incorporated it to GIB, and now you can search those data.
Institute: University of Goettingen
Reference: Genome sequence of Picrophilus torridus and its implications for life around pH 0, Proc. Natl. Acad. Sci. U.S.A. 101, 9091-9096 (2004)
 
Supernig periodic maintenance Jun. 4, 2004
Supernig service will be unavailable during the following date because of the periodic maintenance. Thank you very much for your understanding and cooperation.
Jun. 11 (Fri) 10:00- 13:00
 
The release of the revised H-Invitational Databases Jun. 2nd, 2004
The contents of H-Invitational Database CIB-DDBJ Flat File Server and H-Invitational Database (H-InvDB) (Release number: H-InvDB_1.3) are updated at 31 May, 2004.
  • The revised data for all entries, cDNA and LOCUS, were frozen on 1st May, 2004.
  • The version number of all LOCUS (HIX) and some of cDNA (HIT) entries are changed from ".1" to ".2" by this updating.
  • The file which H-Invitational Identifier (e.g HIT000000001 for cDNA, HIX0000001 for LOCUS) are mapped to the accession number of International Nucleotide Sequence Databases (INSD), DDBJ/EMBL/GenBank, and the information of Data Provider for each cDNA sequences used in H-Invitational is put on FTP site (the file name is "acc2hinv_id.txt.gz").
 
Mycoplasma mobile 163K was added to GIB May 25, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Mycoplasma mobile 163K was released, we incorporated it to GIB, and now you can search those data.
Institute: Harvard Medical School
 
Bacillus anthracis str. Ames 0581 was added to GIB May 21, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Bacillus anthracis str. Ames 0581 was released, we incorporated it to GIB, and now you can search those data.
Institute: TIGR
 
Updates of "Conference on information biology" May. 14, 2004
Following conferences was added to "Conference on information biology".
 
New option of search and analysis service May 10, 2004
In the search and analysis services by E-mail, "email_request_id", a new option to request Request ID notifying mail started.
     Services: FASTA, BLAST, SSEARCH, S&W SEARCH, ClustalW
     Example (request): email_request_id 1
When the request of the Request ID notifying mail is specified in this option, request ID for user's submitted query is sent by e-mail, and the user can confirm the Internet congestion at Traffic information page on Search and Analysis using this ID.
When request ID notification is not selected, an e-mail to notify request ID is not sent to the user. For ClustalW, Request ID had been notified to all users without specifying any options so far.
But, hereafter, if you would like to be notified request ID for your query, you need to specify "email_request_id" option like another homology services.
 
Updates of "Conference on information biology" May 10, 2004
Following conferences was added to "Conference on information biology".
 
Data were added to GIB May 7, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Parachlamydia sp. UWE25 (by University of Vienna), Desulfovibrio vulgaris Hildenborough Photobacterium profundum ss9 (by TIGR), and Listeria monocytogenes 4b F2365 (by CRIBI) were released, we incorporated them to GIB, and now you can search those data.
 
Silkworm Genome in WGS data released Apr. 23, 2004
DDBJ (DNA Data Bank of Japan) released silkworm (Bombyx mori) genomic nucleotide sequence data on Apr. 13, 2004. This data was submitted as WGS (Whole Genome Shotgun) data, and is the first WGS data that DDBJ released.
Please refer to this page for more information about WGS.
This data was submitted by Silkworm Genome Research Program, National Institute of Agrobiological Siences. Accession numbers released from DDBJ are BAAB01000001-BAAB01213289 (213,289 entries 381,906,524 bp). It corresponds to 80% of silkworm genome.
You can retrieve above entries via DDBJ getentry system
Reference
The Genome Sequence of Silkworm, Bombyx mori. DNA Res. 11, 27-35 (2004)
 
Updates of "Conference on information biology" Apr. 19, 2004
Following conferences were added to "Conference on information biology".
 
Release of H-invitational Database Apr. 16, 2004
H-Invitational (Human Full-length cDNA Annotation Invitational) is an international project that human full-length cDNA (complementaryDNA) were performed various bioinformatics analysis and then were assigned a functional annotation, a secondary and tertiary structure of a predicted protein on a cDNA, expression profiles and so on.
The project have been joint-sponsored by the National Institute of Advanced Industrial Science and Technology (AIST), Japan Biological Research Information Center (JBIRC), the Japan Biological Informatics Consortium (JBIC) and the Center for Information Biology and DNA Data Bank of Japan (CIB-DDBJ) National Institute of Genetics, that's now Research Organization of Information and Systems National Institute of Genetics.
The CIB-DDBJ constructs the database, named H-Invitational Database CIB-DDBJ Flat File Server, to release and get a results on functional annotation assigned to full-length cDNA in flat file compatible with the DDBJ flat file format of International Nucleotide Sequence Database with some modification. The Flat Files were prepared by both CIB-DDBJ and JBIRC, called as DDBJ version Flat File and JBIRC version Flat File, respectively, and XML Files was also only made by JBIRC for all of cDNA and LOCUS entries.
All DDBJ and JBIRC version Flat File and XML Files of data can be accessed and downloaded on FTP site.
H-Invitational Database (H-Inv DB) developed by JBIRC is also being released at CIB-DDBJ as mirroring site.
H-Invitational Database CIB-DDBJ Flat File Server
Mirroring H-Inv DB
 
Supernig periodic maintenance Apr. 12, 2004
Supernig service will be unavailable during the following date because of the periodic maintenance.
Apr. 16(Fri) 10:00- 21:00
 
PRF Rel. 96 was released Apr. 9, 2004
PRF (Protein Research Foundation)/SEQ database Release 96 was released on Apr. 9, 2004 at DDBJ. PRF Release 96 consists of 250,321 entries, and the total number of residues reached 88,779,105.
 
Thermus thermophilus HB27 was added to GIB Apr. 7, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Thermus thermophilus HB27 was released, we incorporated it to GIB, and now you can search those data.
Institute: Goettingen Genomics Laboratory
 
PIR rel. 79 was released Apr.6, 2004
PIR rel. 79 was released on Apr. 6, 2004 at DDBJ. PIR rel. 79 consists of 283,367 entries, and the total number of residues reached 96,191,583 aa.
 
Updates of "Conference on information biology" Apr. 5, 2004
Following conferences was added to "Conference on information biology".
 
Statistics [Top 30 organisms according to the total number of nucleotides] Update Apr. 5, 2004
Top 30 organisms according to the total number of nucleotides (- DDBJ rel.57) in DDBJ statistics was updated in accordance with release of DDBJ Rel. 57.
Xenopus tropicalis（a species of clawed frog) which was newly categorized at Rel.57 ranked in 20th. Click the organism name to view the graph of change.
 
New option of search and analysis service Mar. 31, 2004
The search and analysis services by E-mail, a new option "email_request_id" which can request Request ID notifying mail, will start from May 10, 2004.
     Services: FASTA, BLAST, SSEARCH, S&W SEARCH, ClustalW
     Example (request): email_request_id 1
When the request of the Request ID notifying mail is specified by this option, request ID is sent to the user by e-mail. The user can confirm the Internet congestion at Traffic information page on Search and Analysis using this request ID. When not specified, the mail is not sent. For ClustalW, Request ID had been notified to all users so far. But, hereafter, please note that you need to specify "email_request_id" option like as another homology services.
 
DAD rel. 27 was releasedMar. 25, 2004
DDBJ amino acid database (DAD) Release 27 was released on Mar. 25, 2004 at DDBJ. DAD Release consists of 1,743,365 entries, and the total number of residues reached 534,642,804.
FTP site for DB download
 
Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 was added to GIB Mar. 25, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 was released, we incorporated it to GIB, and now you can search those data.
Institute: Instituto Butantan
 
DDBJ Rel. 57 Completed Mar. 23, 2004
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public. We completed DDBJ Release 57 in Mar. 23, 2004. DDBJ Release 57 consists of 32,693,678 entries, and the number of bases reached 38,008,449,840.
FTP site for periodical release and new data download
 
NIG Network service temporary down Mar. 18, 2004
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.
Mar.24(WED) 18:00-19:00
 
Yersinia pestis biovar Mediaevails str. 91001 was added to GIB Mar. 17, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Yersinia pestis biovar Mediaevails str. 91001 was released, we incorporated it to GIB, and now you can search those data.
Institute: The Institute of Microbiology and Epidemiology
 
Methanococcus maripaludis strain S2 was added to GIB Mar. 5, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Methanococcus maripaludis strain S2 was released, we incorporated it to GIB, and now you can search those data.
Institute: University of Washington
Reference: Complete genome sequence of the mesophilic hydrogenotrophic methanogen Methanococcus maripaludis, Unpublished.
 
Bacillus cereus ATCC 10987 was added to GIB Feb. 27, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Bacillus cereus ATCC 10987 was released, we incorporated it to GIB, and now you can search those data.
Institute: TIGR
Reference: The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1.
 
NIG Network service temporary down Feb. 23, 2004
NIG (National Institute of Genetics) network service will be unavailable at the following schedule because of the electric power cut. DDBJ network service and NIG supercomputer (supernig and minerva) service will also be unavailable. Thank you very much for your understanding and cooperation.
From Feb. 28(SAT) 09:00 to Feb. 29(SUN) 18:00
SAKURA temporarily down From Feb. 27(FRI) 18:00 to Mar. 1(MON) 09:00
 
GIB service temporary down Feb. 23, 2004
GIB server will be stopped for a machine maintenance. Thank you very much for your cooperation.
From February 28 (Sat) 17:00 to March 2 (Tue) 18:00
 
PRF Rel. 95 was released Feb. 16, 2004
PRF (Protein Research Foundation)/SEQ database Release 95 was released on Feb. 26, 2004 at DDBJ. PRF Release 95 consists of 243,545 entries, and the total number of residues reached 86,585,811.
 
Data were added to GIB Feb. 10, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data were released, we incorporated them to GIB, and now you can search those data.
Org (Institutes): Reference
Lactobacillus johnsonii NCC 533 (Nestle): The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533, Proc. Natl. Acad. Sci. U.S.A. (2004) In press
Treponema denticola ATCC 35405 (TIGR): Comparison of the genome of the oral pathogen, Treponema denticola, with other spirochete genomes, Unpublished
Wolbachia endosymbiont of Drosophila melanogaster (TIGR):
Mycoplasma mycoides subsp. mycoides SC (KTH): The genome sequence of Mycoplasma mycoides subsp. mycoides SC, type strain PG1T, the causative agent of contagious bovine pleuropneumonia (CBPP), Genome Res. 14, 221-227(2004).
 
Data were added to GIB Feb. 3, 2004
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences. Because the genome sequence data of Bdellovibrio bacteriovorus HD100 and Mycobacterium avium subsp. paratuberculosis str. k10 were released, we incorporated them to GIB, and now you can search those data.
References (Institutes):
Bdellovibrio bacteriovorus HD100 (Max-Planck-Institute): A Predator unmasked: The life cycle of Bdellovibrio bacteriovorus from a genomic perspective, Unpublished.
 
GIB service temporary down Feb. 2, 2004
GIB service will be unavailable at the following schedule because of the server maintenance. Thank you very much for your understanding and cooperation
Feb. 2nd (MON) 10:00-18:00
 
Updates of "Conference on information biology" Feb. 2, 2004
Following conferences were added to "Conference on information biology".
 
Version-up of ClustalW Feb. 2, 2004
ClustalW (multiple alignment and tree-making program) of DDBJ analysis service provided through web and e-mail was updated today.
Version number: 1.80 -> 1.83
By this upgrade, the alignment result in fasta format can be outputted. Moreover, an alignment in the specified region can be executed by using newly added SEQNO_RANGE option. Furthermore, you can specify the display of alignment score. Please use. A part of user interface is also changed by these changes.
Reference: Chenna R. et al. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31(13):3497-500.
 
PRF Rel. 89 was released Jan. 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.
 
Buchnera aphidicola (Baizongia pistaciae) was added to GIB Jan. 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)
 
PIR rel. 75 was released Jan. 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.
 
DAD rel. 22 was released Jan. 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.
 
Supernig periodic maintenance Jan. 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
 
NIG Network service temporary down Jan. 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.
Jan. 15(WED), 2003 18:00 - 19:00
 
Staphylococcus epidermidis ATCC 12228 was added to GIB Jan. 6, 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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