DNA Data Bank of Japan
DDBJ Mail Magazine 
Dec. 21, 2006
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Copyright © 1995-2006
DDBJ All rights reserved.
 ♦ The Variety of Camellia (Camellia japonica) 
I was planning to use the picture of colored leaves at the NIG, however the season changed dramatically and I had missed to take the best season's photo, so this time the picture is about "Camellia".
In Japan, it is said that there are the same number of trees as the names for Camellia. The breed variety is up to 2000 in Japan only and the 6000 variety were confirmed in the world scale.
In addition, the language of flower of Camellia is : Unpretending excellence and Natural beauty
 Camellia

If you have any questions and suggestions about DDBJmag, please don't hesitate to write to ddbjmag@ddbj.nig.ac.jp. We really want to hear from you!!!

 ♦ The announcement of the 3rd DDBJing and PDBjing short training course  
DDBJing is a series of lectures about DDBJ services. DDBJ holds DDBJing, 2-3 times per year, in many parts of Japan to aid users to make the best use of database search and analysis tools provided by DDBJ.
In DDBJing, our staffs generousely give various lectures along with practical demonstrations for deeper understanding of DDBJ services and for concrete exercise of search and analysis tools.

On this coming December 21-22, "The 3rd DDBJing & PDBjing" will be jointly held by DDBJ and PDBj in Tokyo at Tokyo Institute of Technology.
The program of this training course is oriented towards the use of sequence submission facilities and how to use the web services and the studies of DDBJ & PDBj, especially on amino acid and protein analysis. We spared a large amount of time for training participants by using PC, so that they could gain practical skills.

 ♦ Distribution of massive sequence data  
The massive sequence data which were collected by DDBJ and released through the INSD (International Nucleotide Sequence Database) from this October to November are as follows:
Release of new MGA 356,693 entries from Medaka (Oryzias latipes) Nov.14, 2006
A large amount of transcript sequence entries which are categorized as MGA (Mass sequence for Genome Annotation) was released. The newly released data were submitted by a research group of the University of Tokyo. They were derived from Oryzias latipes and were produced by 5'SAGE (5'-end serial analysis of gene expression) method. The total number of sequence entries is 356,693.
Accession numbers for entries; ACAAA0000001-ACAAA0356693 (356,693 entries)
Reference URL:
   http://5sage.gi.k.u-tokyo.ac.jp
   http://medaka.utgenome.org
anonymousFTP:
MGA directory
  • Master record; ACAAA_master
  • Variable record; ACAAA_variable.gz
Project index
 
Release of new sea squirt EST 58,309 entries Nov. 2, 2006
DDBJ newly released sea squirt (Halocynthia roretzi) EST 58,309 entries, which had been submitted by National Institute of Genetics .
The accession numbers are as follows; DB577969-DB636277 (58,309 entries)
These entries were released as DDBJ daily updates on 11/1.
anonymousFTP: Halocynthia_roretzi_EST_061101_1.seq.gz
 
Genome Sequence of Honeybee Nov. 2, 2006
The honeybee genome sequencing consortium made up of 90 institutes reported the genome sequence of the honeybee, Apis melliferaon Nature 443, 931-949 (26 October 2006).
From Japan, RIKEN GSC and others were associated with the consortium. Honeybee EST entries submitted from RIKEN GSC were distributed from DDBJ (See previous report).
  • Genome assemblies are available from following site.
    version 4.0; scaffolds: CM000054-CM000069,
    CH876891-CH878241
    version 3.0; contigs: AADG05000001-AADG05018946
    version 2.0; contigs: AADG04000001-AADG04016028
      scaffolds: CM000054-CM000069,
    CH402995-CH404444
    version 1.2; contigs: AADG03000001-AADG03022771
      scaffolds: CM000054-CM000069,
    CH236967-CH239577
    version 1.1; contigs: AADG02000001-AADG02030074
    version 1.0; contigs: AADG01000001-AADG01015795
  • Genome browsers are available for viewing the genome assemblies at following sites.
    BeeBase;http://racerx00.tamu.edu/bee_resources.html
    NCBI;http://www.ncbi.nlm.nih.gov
    UCSC;http://genome.ucsc.edu
 
The Minimal Genome Sequence, Bacterial Endosymbiont Carsonella Nov. 2, 2006
DDBJ newly released complete genome sequence of Carsonella ruddii which consists of a circular chromosome of 159,662 base pairs. The entry with accession number AP009180 was submitted by RIKEN.
Reference URL (Japanese): http://www.riken.go.jp/r-world/info/release/press/2006/061013/index.html
 

 ♦ INSD-XML upgraded to ver 1.4 
DDBJ upgraded the INSD-XML data format version from 1.3 to 1.4, on October 31, 2006. In DDBJ, INSD-XML data are provided at WWW getentry and anonymous FTP.

1. INSD-XML ver 1.4 is applied on the all data other than MGA at WWW getentry, and is applied on all the data excluding WGS and MGA at anonymous FTP.
2. Output format of getentry was changed from ver 1.3 to 1.4.
When you do the search specifying DNA as the target database and INSD as the output format, the results are outputted in the ver 1.4 format.
3. At anonymous FTP, both 1.3 and 1.4 format data are available until the distribution of DDBJ release 68 (around the end of this year).
INSD-XML version 1.3
INSD-XML version 1.4
4. Hierarchy of anonymous FTP site (where XML data are placed) was also reconstructed. DDBJ release and DDBJ new data are subject to this change.
  • DDBJ-XML was moved from xml/ to xml/ddbjxml/
  • INSD-XML was moved from insd/ to xml/insdxml
  • To obtain the latest version INSD-XML data, please visit xml/insixmlcurrent/
    xml/:DDBJ-XML data allocated*
    xml/insd/: INSD-XML v1.3 data allocated*
    xml/ddbjxml/: DDBJ-XML data allocated
    xml/insdxml/: INSD-XML data allocated
    xml/insdxml/v1.3/: INSD-XML v1.3 data allocated*
    xml/insdxml/v1.4/: INSD-XML v1.4 data allocated
    xml/insdxml_current/: INSD-XML latest version data directory
    * xml/ , xml/insd/ and xml/insdxml/v1.3/ are deleted after the release of DDBJ release68 (scheduled in the end of December, 2006)


 ♦ Upgrading the computer system of the National Institute of Genetics (NIG) 
The current computer system of NIG was installed six years ago. It was composed of the latest possible set of high performance servers, a vector-parallel processor, a mass storage system and others at that time. However, the system has gradually become obsolete and cannot really meet now the current mounting demands for data submission, management, storage, retrieval and analysis. Therefore, NIG will replace it with an upgraded system during late February to early March, 2007.
The upgraded computer system is composed of various high-performance servers and cluster machines for various purposes, a mass external storage system, personal computers and various peripheral equipments for networks and others. The total capacity of this system ranks high by the present standards. The new system will thus make it possible for users inside NIG and outside to perform more rapid and efficient data submission, retrieval and analysis. It will also enable the DDBJ staff to carry out more effective and efficient data annotation, processing and management.
Consequently, certain services at DDBJ will be temporarily suspended, changed or terminated from the beginning of January, 2007. The details will be announced on the DDBJ homepage (http://www.ddbj.nig.ac.jp/replace/replace-e.html) by the end of December, 2006.
Thank you very much for your understanding and cooperation in advance.

 ♦ Illegal values were included in CONTIG lines within a part of ultra-contig and chromosome entries derived from Oryzias latipes (Japanese medaka) WGS data  
Part of ultra-contig and chromosome entries, which were constructed by using Oryzias latipes (Japanese medaka) WGS data, contained illegal values at the location of piece entries in CONTIG lines.
  • The accession and version numbers of wrong ultra-contig and chromosome entries were listed below. At present, all the wrong entries were replaced with corrected ones. The version number of the corrected ultra-contig entries is ".4".
    List of accession and version numbers of the wrong ultra-contigs (42 entries)
    DF076134.3, DF076146.3, DF076156.3, DF076165.3, DF076168.3, DF076174.3,
    DF076189.3, DF076197.3, DF076201.3, DF076203.3, DF076205.3, DF076217.3,
    DF076230.3, DF076245.3, DF076247.3, DF076249.3, DF076256.3, DF076258.3,
    DF076269.3, DF076279.3, DF076281.3, DF076285.3, DF076298.3, DF076306.3,
    DF076312.3, DF076313.3, DF076318.3, DF076341.3, DF076366.3, DF076379.3,
    DF076386.3, DF076387.3, DF076391.3, DF076408.3, DF076411.3, DF076417.3,
    DF076418.3, DF076425.3, DF076430.3, DF076449.3, DF076456.3, DF076457.3
    List of accession and version numbers of the wrong chromosome (20 entries)
    DG000001.1, DG000002.1, DG000003.1, DG000004.1, DG000005.1, DG000006.1,
    DG000008.1, DG000009.1, DG000010.1, DG000011.1, DG000012.1, DG000013.1,
    DG000014.1, DG000016.1, DG000018.1, DG000019.1, DG000021.1, DG000022.1,
    DG000023.1, DG000024.1

We have replaced 24 entries of all chromosomes with updated version like below in order to control the chromosome versions uniformly
previous version--> updated version
DG000001.1-DG000024.1-->DG000001.3-DG000024.3
DG000001.2-DG000024.2-->DG000001.4-DG000024.4
DG000001.2-DG000024.2 were transferred to DG000001.4-DG000024.4 without any changes except for the date of LOCUS line and version number

The below three files, which were distributed from our anonymous FTP site: ftp://ftp.ddbj.nig.ac.jp/ddbj_database/mass/Oryzias_latipes_CON/, contain the entries including the illegal CONTIG lines. Please be careful not to use the three files. At present, the three files were removed from the FTP site and replaced with the revised files.
ftp://ftp.ddbj.nig.ac.jp/data base/mass/Oryzias_latipes_CON/
Oryzias_latipes_CON_060524_1.seq.gz
Oryzias_latipes_CON_060531_1.seq.gz
Oryzias_latipes_CON_060605_1.seq.gz

  • You can see the revised file list by clicking here.
  • In addition, Oryzias_latipes_CON_060615_1.seq.gz that includes DG000001.2-DG000024.2 was replaced with Oryzias_latipes_CON_061018_1.seq.gz that includes DG000001.4-DG000024.4.

We apologize for your inconvenience.  

 ♦ The report of the SPAM mail trouble. 
We really apologize the users for our emergent correspondence against huge amount of SPAM mails which targeted the National Institute of Genetics mail server for 20 days from the beginning of this November.
The SPAM mail trouble were caused by the continuous massive amount of e-mail reception for several days. The amount of e-mail reception was 3 to 6 times the normal rate and at the peak time, it went up to 10 times per hour. In response to this unusual situation, we had to stop all e-mail reception from outside temporarily. After having a temporary stop of e-mail reception, we have rejected e-mails which was sent from the free e-mails such as yahoo.com, hotmail.com, gmail.com, etc. from November 11 to 20.
Because of this trouble, it takes long time to receive the inquiry mail or the inquiry mails were returned to the users as the error mails. So, we had been in difficult time to answer the query mails immediately.
The amount of e-mail reception was gradually decrease from November 15 and it became normal now, so we canceled the restriction of free mail reception on November 20.
SPAM mails are increasing year by year and its damage is considered as the social problem. This kind of trouble might occur again in the future, as countermeasures, NIG schedule to intensify the mail server and consider the anti-virus software to prevent the effect to the minimum.
We apologize for your inconvenience and thank you for your cooperation and understanding in advance.

 ♦ Participation to [Genome HIROBA 2006] 
DDBJ presented posters and introduced our services at [Genome HIROBA 2006(a kind of genome symposium for the public)] from November 4-5, in Tokyo.
This symposium purposed to introduce genomes and its latest study to the people who are mostly beginners in the Bioinformatics fields.
In the symposium, not only presenting posters and distributing information materials, DDBJ staffs explained and introduced its roles and how beginners can use the DDBJ services with the example of microbes.
 Genome HIROBA 2006

 ♦ Suspension of the DDBJ activity during the New Year Holidays 
We at DDBJ will temporarily close our business for the New Year Holidays in the following schedules, according to the Japanese custom, and resume the normal business on January 4th, 2007.
Please note in particular that SAKURA will also stop in operation for a while (see below).
However, the computer search and analysis and FTP are available during the holidays.
DDBJ activity suspension: from December 29th, 2006 to January 3rd, 2007
SAKURA suspension: from December 27th, 2006 to January 4th, 2007
data release suspension: from December 27th, 2006 to January 4th, 2007
Thank you very much for your understanding and cooperation.
We wish you a Happy New Year.

December 4th, 2006
DNA Data Bank of Japan

Published by: DNA Data Bank of Japan (DDBJ)
  Center for Information Biology and DNA Data Bank of Japan (CIB-DDBJ)
National Institute of Genetics (NIG)
Research Organization of Information and Systems
1111 Yata, Mishima, Shizuoka 411-8540, JAPAN
Last modified: Oct. 07, 2011