What’s New(2000)

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 biologySep. 1, 2000
INTERNATIONAL WORKSHOP ¡ÖIntegration 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,
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 join 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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