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Contact Us
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Copyright © 1995-2006
DDBJ All rights reserved. |
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New service "SQmatch" was started Dec. 27, 2000
- A new service called "SQmatch" is now available in DDBJ WWW site.
This service is matching a regular expression against sequences in Database.
It is effective for the short sequences and such as those including "N"
(undetermined).
The URL is
http://ftp2.ddbj.nig.ac.jp:8080/sqmatch_en.html.
This has a link from [Database Searches and Data Analyses] of DDBJ Home Page.
-
Updates of "Conference on information biology" Dec. 20, 2000
- Bio China 2001 (Aug. 22 - 25) was
added to "Conference on information biology".
-
Suspension of the DDBJ activity during the New Year Holidays Dec. 6th, 2000
- We at DDBJ will suspend our business during the New Year Holidays
from December 29th, 2000 to January 3rd, 2001.
We will stop most activities including receiving data and issuing
accession numbers during that period, and resume the normal business
on January 4th, 2001.
- Please note in particular that SAKURA will stop in operation from December 26th, 2000 to January 3rd, 2001.
- Thank you very much for your understanding and cooperation.
- We wish you a Happy New Century.
- DNA Data Bank of Japan
- DDBJ Rel. 43 Completed Oct. 30, 2000
- The nucleotide sequence database collected and maintained by
DDBJ is quarterly released online to the public and distributed in
the magnetic media. We completed DDBJ Release 43 in Oct. 2000.
DDBJ Release 43 consists of 8,666,551 entries, and the number of
bases reached 10,034,532,698.
- "Silver Project: Ape Genome Sequencing" was released Oct. 26, 2000
- A New service called "Silver Project" is now available in DDBJ WWW site.
Silver Project was constructed by Saitou Lab at Laboratory of Evolutionary
Genetics, National Institute of Genetics.
The URL is
http://sayer.lab.nig.ac.jp/~silver/index.html.
This has a link from [Database Searches and Data Analyses] and [Links
to Other Databases] of DDBJ Home Page.
- PIR Rel.66 was released Oct. 19, 2000
- PIR Rel. 66 was released on Oct. 19, 2000 at DDBJ.
PIR Rel.66 consists of 195,891 entries, and the total number of
residues reached 67,900,656 aa.
- Thermoplasma acidophilum was added to GIB Oct. 19, 2000
- GIB (Genome Information Broker
for Microbial Genomes) provides a comprehensive view of the complete
microbial genome sequences.
Because the genome sequencedata of Thermoplasma acidophilum was
released, we incorporated it to GIB,and now you can search those data.
- Supernig periodic maintenance Oct. 12, 2000
- Supernig service will be unavailable during the following date because
of the periodic maintenance.
- We appreciate your cooperation.
- Oct. 20 (Fri) 10:00-21:00
- Bacillus halodurans C-125 and
Halobacterium sp. NRC-1 were added to GIB Oct. 10, 2000
- GIB
(Genome Information Broker for Microbial Genomes) provides a comprehensive
view of the complete microbial genome sequences.
Because the genome sequencedata of Bacillus halodurans C-125 and
Halobacterium sp. NRC-1 were released,
we incorporated them to GIB,and now you can search those data.
- Buchnera sp. APS was added to GIB Sep. 18, 2000
- GIB
(Genome Information Broker for Microbial Genomes) provides a comprehensive
view of the complete microbial genome sequences.
Because the genome sequencedata of Buchnera sp. APS was released,
we incorporated it to GIB,and now you can search those data.
- Supernig periodic maintenance Sep. 14, 2000
- Supernig service will be unavailable during the following date because of
the periodic maintenance.
- We appreciate your cooperation.
- Sep. 22 (Fri) 12:00 - 21:00
- Pseudomonas aeruginosa PA01 was added to GIB Sep. 7th, 2000
- GIB
(Genome Information Broker for Microbial Genomes) provides a comprehensive view
of the complete microbial genome sequences.
Because the genome sequencedata of Pseudomonas aeruginosa PA01 was
released, we incorporated it to GIB,and now you can search those data.
- New genome data analyses database "GTOP" was released Sep. 1st, 2000
- A new service called "GTOP (Genome TO Protein structure and function)"
is now available in DDBJ WWW site.
- This database was constructed by Laboratory for Gene-Product Informatics
in National Institute of Genetics.
- The URL is
http://spock.genes.nig.ac.jp/~genome/gtop.html.
This has a link from [Database Searches and Data Analyses] of DDBJ Home Page.
- INTERNATIONAL WORKSHOP "Integration of
Biodiversity and Genome Technology for Crop Improvement" was added to
Conference on information biology Sep. 1, 2000
-
INTERNATIONAL WORKSHOP 「Integration of Biodiversity and Genome Technology
for Crop Improvement」 (November 28-December 1, 2000) was added
to "Conference on information biology".
- Scheduled stop of DDBJ network services Sep. 1st, 2000
- In order to conduct the maintenance work, all network services in DDBJ
will be stopped the following date.
- Date: From 10:00 ,to 15:00, September 17 (Sun)
- Thank you for your understanding and cooperation.
- International Conference on Structural
Genomics 2000 was added to Conference on information biology Aug. 29, 2000
- International Conference on
Structural Genomics 2000 (November 2-5, 2000) was added to
"Conferenceon on information biology".
- PIR Rel.65 was released Aug. 25, 2000
- PIR Rel.65 was released on Aug. 25, 2000 at DDBJ.
PIR Rel.65 consists of 182,106 entries, and the total number of residues
reached 63,460,219.
- SWISS-PROT Rel.39 was released Aug. 21, 2000
- SWISS-PROT Rel.39 was released on Aug. 18, 2000 at DDBJ.
SWISS-PROT Rel.39 consists of 86,593 entries, and the total number of residues
reached 31,411,157.
- supernig periodic maintenance Aug. 17, 2000
- Supernig service will be unavailable during the following date because of
the periodic maintenance.
We appreciate your cooperation.
- Aug. 25 (Fri.) 12:00 - 21:00
- RECOMB 2001 was added to Conference on
information biology Aug. 15, 2000
- RECOMB 2001 (April 21-24, 2001)
was added to "Conference on information biology".
- Vibrio cholerae N16961 was added to GIB Aug. 7th, 2000
- GIB
(Genome Information Broker for Microbial Genomes) provides a comprehensive view
of the complete microbial genome sequences.
Because the genome sequencedata of Vibrio cholerae N16961 was released,
we incorporated it to GIB,and now you can search those data.
- DAD Rel. 12 was released Aug. 2nd, 2000
- DDBJ amino acid database (DAD) Release 12 was released on Aug. 1st, 2000
at DDBJ.
DAD Release 12 consists of 567,195 entries, and the total number of residues
reached 176,496,181.
- Chlamydophila pneumoniae strain J138 was added to GIB Jul. 25, 2000
- GIB
(Genome Information Broker for Microbial Genomes) provides a comprehensive view
of the complete microbial genome sequences.
Because the genome sequencedata of Chlamydophila pneumoniae strain J138
was released, we incorporated it to GIB, and now you can search those data.
- DDBJ Rel. 42 Completed Jul. 21, 2000
- The nucleotide sequence database collected and maintained by
DDBJ is quarterly released online to the public and distributed in
the magnetic media. We completed DDBJ Release 42 in Jul. 2000.
DDBJ Release 42 consists of 7,554,995 entries, and the number of
bases reached 9,171,507,604.
- Xylella fastidiosa was added to GIB Jul. 19, 2000
- GIB
(Genome Information Broker for Microbial Genomes) provides a comprehensive view
of the complete microbial genome sequences.
Because the genome sequencedata of Xylella fastidiosa was released,
we incorporated it to GIB,and now you can search those data.
- supernig periodic maintenance Jul.7th, 2000
- Supernig service will be unavailable during the following date because of
the periodic maintenance.
We appreciate your cooperation.
- Jul. 21 (Fri) 12:00 - 23 (Sun) 15:00
- New Version of getentry on DDBJ web was released Jul. 4th, 2000
- "getentry" is
a kind of index search application program on DDBJ web and E-mail server.
New version of getentry on DDBJ web was released on May 9th.
Additional function was related to the view of CON data.
Now, you can select the view of CON entry, be transferred (by ftp) or displayed
directly.
If there are gaps between entries,
> gap()
//
is displayed.
- WARNING)
- A large amount of data will be transferred if you select "display".
So, please be careful about memory overflow on the client side.
Also, the combined DNA sequence will not be created if there are gaps between
entries.
- Improvement of homology search service Jul. 3rd, 2000
- DDBJ homology
search services
(FASTA, BLAST, PSI-BLAST, SSEARCH) were updated on June 19th.
The interfaces were changed and Blast server got faster than before.
- The default target division was changed from "all DNA data" to "all except
EST, HTG, GSS, STS, SYN, UNA divisions".
It is also effective when "DDBJ ALL" or "DDBJ updates" is selected.
By this change, you can search well-annotated DNA sequence data efficiently.
- supernig periodic maintenance Jun. 8th, 2000
- Supernig service will be unavailable during the following date because of the periodic maintenance.
We appreciate your cooperation.
- Jul. 16 (Fri.) 12:00-21:00
- "DDBJ/CIB Human Genomics Studio" was released May 31, 2000
- We developed a homepage
"DDBJ/CIB Human Genomics Studio", which is a product of research and
development project of DDBJ (DNA Data Bank of Japan) and CIB (Center for
Information Biology, National Institute of Genetics).
It aims at providing human genomic sequences and results of genome informatics
analyses. In particular, we are collecting and assembling human draft sequences,
which are rapidly increasing in number, to construct the entire sequences of
human chromosomes. The results will be placed in this homepage soon.
- DAD Rel. 11 was released May 12, 2000
- DDBJ amino acid database (DAD) Release 11 was released on May 11, 2000 at
DDBJ. DAD Release 10 consists of 514,763 entries, and the total number of
residues reached 158,049,461.
- supernig periodic maintenance May 12, 2000
- Supernig service will be unavailable during the following date because of
the periodic maintenance.
We appreciate your cooperation.
- May 19, 2000 (Fri.) 10:00-21:00
- The Human Chromosome 21 Sequencing Completed May. 12, 2000
- The Chromosome 21 Mapping and Sequencing Consortium completed the sequencing
of the human chromosome #21 and submitted the data to DDBJ/EMBL/GenBank
International Nucleotide Sequence Database.
The Chromosome 21 Mapping and Sequencing Consortium consists of Japanese and
German teams.
- Japanese team:
- * RIKEN Genomic Sciences Center,
Human Genome Research Group ( Headed by Dr. Yoshiyuki Sakaki)
- * Keio University School of
Medicine, Dept. of Molecular Biology ( Headed by Dr. Nobuyoshi Shimizu)
- German team:
- - Institute of Molecular Biotechnology
- - GBF, Dept. of Genome Analysis
- - Max-Planck Institute for
Molecular Genetics
In total we have made public 106 entries
( about 33 Mbases) of HUM division sequence data. Japanese team was in charge
of 75 entries.
We constructed the CON entry assembled by 105 entries on q arm of Chr #21.
Accession numbers is BA000005. From below, the DNA sequence(s) having
reference to BA000005 can be transferred (by ftp) or displayed directly.
o transfer all the relevant DDBJ entries in DDBJ format
o transfer all the DNA sequences separately in FASTA format
o display all the DNA sequences separately in FASTA format
WARNING)
A large amount of data will be trasferred if you select "display".
So, please be careful about memory overflow on the client side. Also, the
combined DNA sequence will not be created if there are gaps between entries.
About CON division:
The CON division is to show the order of related sequences in a genome, and
expressed by join and the accession numbers of the sequences.
The contents of the CON division are compiled by the three data banks not by
the data submitter.
Submitted by RIKEN, 54 entries
AP001660, AP001666, AP001667, AP001669, AP001670, AP001671, AP001672,
AP001674, AP001675, AP001676, AP001677, AP001678, AP001679, AP001680,
AP001681, AP001683, AP001684, AP001685, AP001686, AP001687, AP001688,
AP001689, AP001690, AP001691, AP001692, AP001693, AP001694, AP001695,
AP001705, AP001706, AP001708, AP001709, AP001710, AP001711, AP001712,
AP001713, AP001714, AP001715, AP001716, AP001717, AP001718, AP001719,
AP001720, AP001721, AP001728, AP001729, AP001730, AP001731, AP001742,
AP001744, AP001750, AP001759, AP001760, AP001761,
Submitted by Keio University, 21 entries
AP001696, AP001697, AP001698, AP001699, AP001700, AP001724, AP001725,
AP001726, AP001727, AP001732, AP001741, AP001743, AP001745, AP001746,
AP001747, AP001748, AP001749, AP001751, AP001752, AP001753, AP001754,
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- SAKURA service reopening May. 8, 2000
-
We reopened SAKURA (DDBJ DNA
Data submission system) service that was stopped from April 29 to May 7
because of the upgrade.
We appreciate your cooperation.
- DDBJ Rel. 41 Completed May. 1st, 2000
- The nucleotide sequence database collected and maintained by DDBJ is
quarterly released online to the public and distributed in the magnetic media.
We completed DDBJ Release 41 in Apr. 2000.
DDBJ Release 41 consists of 5,962,608 entries, and the number of bases reached
6,409,581,885.
- From the present release we include a new division, CON. The CON division
is to show the order of related sequences in a genome, and expressed by join
and the accession numbers of the sequences. The contents of the CON division
are compiled by the three data banks not by the data submitter.
- New prefix of accession number, BA and BB were added from this release.
BA was used by DDBJ for CON data. BB will be used by DDBJ for EST data.
- PIR Release 64 was released Apr. 24, 2000
- PIR amino acid database Release 64 was released on line to the public on Apr. 21, 2000 at DDBJ.
PIR Release 64 consists of 178,058 entries, and the total number of residues reached 61,890,410.
- Temporary stop and upgrade of SAKURA service Apr. 20, 2000
- SAKURA (DDBJ DNA Data submission system) service will be stopped during the following period because of the upgrade of SAKURA.
Apr.29 (Sat) - May 7 (Sun)
- The upgraded service of SAKURA will start after the period.
The new SAKURA system accepts almost all features/qualifiers that DDBJ/EMBL/GenBank provide. In addition it checks input data more strictly, which makes you find an error in your input data more easily.
As a result of many changes in the new system, the data format of the new system is not compatible with that of the current system.
If you are planning to do sequential submission, please complete it before the current system is stopped, or start the registration after the new SAKURA is released.
We appreciate your cooperation.
- The news and attention of the SAKURA upgrade Apr. 14, 2000
- These are for example the input of almost all Feature/Qualifier's, and the strict error check.
Because there have been many changes in the new system, new system's data format isn't compatible with current system.
If you are planning continuous registration, please start registration after new SAKURA is introduced to the public, or immediately finish continuous registration.
If you have already started continuous registration, please complete it on current system at once, or stop it and reenter on the new system.
We intend to release the new SAKURA on April 20.
- supernig periodic maintenance Apr.
13, 2000
- Supernig service will be unavailable during the following date because of the periodic maintenance. We appreciate your cooperation.
- Apr. 21 (Fri.) 12:00 - 21:00
- Neisseria meningitidis Z2491 was added to GIB Apr. 12, 2000
- GIB
(Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences.
Because the genome sequencedata of Neisseria meningitidis Z2491 was released,
we incorporated them to GIB,and now you can search those data.
- Chlamydophila pneumoniae AR39, Chlamydia muridarum and Neisseria meningitidis
were added to GIB Mar. 15, 2000
- GIB
(Genome Information Broker for Microbial Genomes)
provides a comprehensive view of the complete microbial genome sequences.
Because the genome sequencedata of Chlamydophila pneumoniae AR39,
Chlamydia muridarum and Neisseria meningitidis were released,
we incorporated them to GIB,and now you can search those data.
- supernig periodic maintenance Mar. 10, 2000
- Supernig service will be unavailable during the following date because of the periodic maintenance. We appreciate your cooperation.
- Mar. 17 (Fri.) 12:00 - 21:00
- SRS 6.0.5.1 was released Feb. 28, 2000
- SRS 6.0.5.1 was released on February 2.
- You can search the following using the current version of SRS.
- - Key word search for every field
- example) If you want to retrieve entries containing "acetylchol" and "receptor"
but not "muscarinic" in "definition" line,
- how to specify query: acetylchol* & receptor* ! muscarinic
- - Numerical range appointment search
- example) If you want to retrieve entries whose length are less than
20000 and more than 10000,
- how to specify query: 10000 : 20000
- - Range appointment search of a date
- example) If you want to retrieve entries which were updated on January
1 2000 and later,
- how to specify query: 1-jan-2000 :
- Please read here (http://srs.ddbj.nig.ac.jp/doc/srsQueryLanguage.html) in detail.
- *Attention
Feature informations are not covered when you select "AllText" field.
If you want to search for all Feature informations, please use FeatureDescription.
Therefore, If you want to search for all fields, please search AllText and Feature Description together.
- Database
| Sequence | DDBJ, DDBJNEW, DAD, DADNEW, SWISSPROT, PIR |
| Sequence Related | PROSITE, PROSITEDOC, BLOCKS, PRINTS,
PFAMA, PFAMB, SWISSPFAM, PFAMHMM, PFAMSEED, PRODOM, ENZYME |
| Protein 3D Struct | PDB, HSSP, FSSP |
| Metabolic Pathway | PATHWAY, LENZYME, LCOMPOUND |
- You can also use CLUSTALW/BLASTP from the search results of SRS for some databases.
- Updates of DDBJ
homology search service Feb. 28, 2000
- DDBJ homology search service was updated on February 9.
- - We changed FASTA program to FASTA32t09.
Now you can search both directions (3'<->5') at the same time when you select "DNA".
Besides you can choose "Highest Expect" and "Lowest Expect" options.
- - You can choose "DIVISION" and "Organism of EST division" when you select Database "DDBJ ALL" or "DDBJ Updates".
Meanwhile, "DDBJ Release" was deleted from selectable database.
- - We reinforced the checking function of E-mail domain name address when you input your email address to receive your search results.
- Ureaplasma urealyticum and
Campylobacter jejuni NCTC11168 were added to GIB Feb. 23, 2000
- GIB (Genome Information Broker
for Microbial Genomes) provides a comprehensive view of the complete microbial
genome sequences. Because the genome sequencedata of Ureaplasma urealyticum
and Campylobacter jejuni NCTC11168 were released, we incorporated them
to GIB,and now you can search those data.
- get-entryNew Version of get-entry was released Feb. 22, 2000
- New Version of get-entry was released on February 18.
- Additional functions are the followings.
- - search and view CON divison entries.
- - view and transmit sequence data defined in a "CON" entry at the same time.
- - transmit piece DDBJ format entries defined in a "CON" entry at the same time.
- - link to corresponding entries via those accession numbers defined with joi
n of a CON entry.
- - link to corresponding entries via CON accession number described as secondary one of piece entry.
- - search by "product" name.
- Notes.
Currently you can search only CON entries (about 7,000) which were released by GenBank.
- - reduced line number such as titles and can view the input column from the initial window.
- - changed way of number selection from radio button to menu.
- - changed some item names of menu selection.
- supernig periodic maintenance Feb. 10, 2000
- Supernig service will be unavailable during the following date because of the
periodic maintenance.
We appreciate your cooperation.
- Feb. 18 (Fri.) 12:00 - 21:00
- DAD Rel.10 was released Feb. 9, 2000
- DDBJ amino acid database (DAD) Release 10 was released on Feb. 8, 1999 at DDBJ.
DAD Release 10 consists of 5,388,125 entries, and the total number of residues
reached 4,762,696,173.
- DDBJ Rel. 40 Completed Feb. 3rd, 2000
- The nucleotide sequence database collected and maintained by DDBJ is quarterly
released online to the public and distributed in the magnetic media.
We completed DDBJ Release 40 in Jan. 2000.
DDBJ Release 40 consists of 5,388,125 entries, and the number of bases reached
4,762,696,173.
- DDBJ terminated the RNA division.
The extant RNA data were redistributed according to the category of the organism.
- New prefix of accession number, AZ was added from this release.
AZ will be used by GenBank for GSS data.
- supernig periodic maintenance Jan. 14, 2000
- Supernig service will be unavailable during the following date because of the periodic maintenance.
We appreciate your cooperation.
- Jan. 21 (Fri.) 12:00 - 21:00
- Deinococcus radiodurans was added to GIB Jan. 5th, 2000
- GIB (Genome Information Broker for Microbial Genomes) provides a comprehensive view of the complete microbial genome sequences.
Because the genome sequencedata of
Deinococcus radiodurans were released, we incorporated them to GIB,and now you can search those data.
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