DNA Data Bank of Japan
DDBJ Mail Magazine 
March 3, 2006
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 ♦ Full-blown Cherry Blossom will be coming soon !! 
cherry blossom This is the web version of the bimonthly DDBJ Mail Magazine (Number 24th).
Have you been feeling good in these days? It's getting warmer and warmer. For the people with hay fever, it might be a beginning of the unpleasant season (or some might feel like a spring nightmare !). Yet, it is true that plants are ready to welcome the beautiful spring !!
The picture is the earliest cherry blossom in NIG (National Institute of Genetics).
If you have any questions and opinions about DDBJmag, please don't hesitate to write to ddbjmag@ddbj.nig.ac.jp. We really want to hear from you!!!!

 ♦ 14th DDBJing & 2nd PDBjing in Osaka 
DDBJing & PDBjing DDBJ has irregularly hold DDBJing (a series of lectures about DDBJ services) in many parts of Japan, so that users can make the best use of the database search and analysis services at DDBJ. Please note that the lectures are basically given in Japanese.
We have successfully accomplished the 14th DDBJing & 2nd PDBjing at Osaka on February 2-3,2006. This time, DDBJ, PDBj and IPR(Institute for Protein Research) jointly held the 14th DDBJing & 2nd PDBjing. The lectures were about 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.
We are planning to hold another DDBJing sometime in this year 2006, so please visit DDBJ Home Page frequently to check for the exact date and venue.

 ♦ 5th Japan-Korea-China Bioinformatics Training Course 
"The 5th Japan-Korea-China Bioinformatics Training Course" will be held at the Center for Information Biology and DNA Data Bank of Japan (CIB-DDBJ) at the National Institute of Genetics (NIG) in March 14-17, 2006.
This course is oriented for Japanese, Korean, and Chinese young researchers. The number of Japanese trainees is limited to 10. The trainee is expected to be either a graduate student or a postdoctoral fellow working in bioinformatics or in related fields. All participants must be fluent in English. The deadline of the application was closed on February 20.
This year's Training Course has already closed, but we plan to hold this kind of course in next year. If you have interest, please pay attention to our HP.
Application:
  • Venue: National Institute of Genetics, Mishima, Japan
  • Dates: March 14th to March 17th, 2006
  • Trainees: Ten trainees from each of the three countries, 30 in total.
  • Language: English
  • Fee: free


 ♦ ARSA : Functional Improvement 
ARSA (All-round Retrieval of Sequence and Annotation) is the keyword search system provided by DDBJ under trial operation.
By using a high-speed XML type database searching engine, there are two distinctive characteristics in ARSA. It enables users to select complex searching conditions and specify the Feature/Qualifier flat file (FF) form defined by INSDC as the detailed searching condition.
The service had been temporarily unavailable from Jan. 10 to 19, due to a system upgrade maintenance work. According to this upgrade work, the following points are improved in the service.
  • ARSA can be used for 24 hours without break
  • Results (Flatfile, XML) are displayed faster than before
Thank you for your patience for the inconvenience of the temporal suspension of the service. Currently the service is fully operative and we like to hear from you if you have any questions.

 ♦ Release of the complete genome sequence of Escherichia coli K-12 strain W3110 
The complete genome sequence of Escherichia coli K-12 strain W3110 was released from DDBJ. Accession number for this sequence is AP009048.
As to E. coli K-12 genome, Monica Riley of Marine Biological Laboratory (MBL) worked as a leader of the annotation workshop that was held in 2003 and 2005 at MBL. From Japan, researchers of NAIST (Nara Institute of Science and Technology), NIBB (National Institute for Basic Biology) and DDBJ participated in the workshop. Accurate and complete annotations were assigned to the latest high quality genomic sequences of two E. coli K-12 strains (strain W3110 and MG1655 whose genome sequences were determined in Japan and U.S.A, respectively).
The results of the workshop have been already published as a paper in Nucleic Acids Research.
Riley, M., et al. "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005", Nucleic Acids Res., 34, 1-9 (2006).
E. coli is one of the most important organisms for various biological fields, such as molecular biology, genome sequencing, systems biology, etc. The release of accurate and complete E. coli genome annotation provides researchers with meaningful information in the science field.
Reference URL:
Functional Genomic Analysis of E. coli in Japan
MBL News
GIB Escherichia coli K-12 W3110

 ♦ The current situation of microbe Genome submissions and update. 
Oct., 2005 4
Nov., 2005 12
Dec., 2005 28
Jan., 2006 48
The number of released microbe genome submissions is steadily increasing since 1995. As a result, we have released 305 genomes (including 3 Eukaryotes ) from Genome Information Broker (GIB) on January, 2006. In addition to the new submissions, updating of previously released data has been also remarkably increased (as you see in the Table). Before downloading a microbial genome, please check that the data corresponds to the latest version.

 ♦ DDBJ Rel. 64 completed and partition of large index files 
The nucleotide sequence database collected and maintained by DDBJ is released online quarterly. We completed the DDBJ Release 64 in Dec. 28, 2005. DDBJ Release 64 consists of 52,272,669 entries, and the number of bases reached 56,098,558,378.
In the present release, some of the index files (ddbjacc.idx, ddbjjou.idx, and ddbjkey.idx) are larger than 2 GB in file size. From this release, we have decided to divide over 2GB files into 1.5GB unit. (This time, we didn't divide the ddbbjen.idx.)
For details, please refer to Release note.
FTP site for periodical release and new data download

 ♦ Report for DDBJ activities in NAR  
The recent DDBJ activities were introduced in the special database issue of Nucleic Acids Research Vol.34 Database Issue (Jan. 1).
  • Report for Overall activities of DDBJ in 2005
    "DDBJ in preparation for overview of research activities behind data submissions."
    Kousaku Okubo, Hideaki Sugawara, Takashi Gojobori and Yoshio Tateno
    Nucleic Acids Research, 2006, Vol. 34, Database issue D6-D9
    (Summary) INSDC collaboration,introduction of newly released databases, new achievements, especially , indexing for breakdown statistics are released in DDBJ HP. (PMID: 16381940)
  • Introduction of the new database:BodyMap-Xs
    "BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression."
    Osamu Ogasawara, Makiko Otsuji, Kouji Watanabe, Takayasu Iizuka, Takuro Tamura, Teruyoshi Hishiki, Shoko Kawamoto, and Kousaku Okubo
    Nucleic Acids Research, 2006, Vol. 34, Database issue D628-D631
    (Summary) BodyMap-Xs (a database for cross-species gene expression comparison based on EST data) was created and released.(PMID: 16381946)
  • Introduction of the new database:Rap-DB
    "The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information."
    Hajime Ohyanagi, Tsuyoshi Tanaka, Hiroaki Sakai, Yasumasa Shigemoto, Kaori Yamaguchi, Takuya Habara, Yasuyuki Fujii, Baltazar A. Antonio, Yoshiaki Nagamura, Tadashi Imanishi, Kazuho Ikeo, Takeshi Itoh, Takashi Gojobori, and Takuji Sasaki
    Nucleic Acids Research, 2006, Vol. 34, Database issue D741-D744
    (Summary) The RAP-DB, a database for highly curated rice annotations was made public in last December.. (PMID: 16381971)


 ♦ DDBJ new staff ! 
Dr. Osamu Ogasawara (Assistant Professor of the Laboratory for Gene-Expression Analysis) joined DDBJ as the 14th staff. He had been a project researcher at DDBJ, who previously was working at the Information and Mathematical Science Laboratory Inc.
He said that he was hoping to contribute to DDBJ activities, especially on the improvement of database searching systems.

 ♦ "Flat file (EMBL)" was removed from getentry output format options 
getentry is the data retrieval system provided by DDBJ through web and E-mail.
"Flat file (EMBL)" is one of the result output formats which are available when "DNA DATABASE" is selected as the target database. However, as the users utilizing this output file have been decreased, DDBJ decided to remove "Flat file (EMBL)" format from the options on Jan. 16, 2006.
Please select other formats from the options listed below from this out.
DNA DATABASE
- Flat file (DDBJ)
- Complete nucleotide sequence FASTA
- CDS amino acid sequence FASTA
- CDS nucleotide sequence FASTA
- Quality Value - DDBJ-XML
- INSD-XML
Protein DATABASE
- Amino acid sequence FASTA
- Nucleotide sequence FASTA (for DAD)

 ♦ Errata at DDBJ services 
Homology search error at X. tropicalis (formerly S. tropicalis) of EST division
In DDBJ's homology search programs (WWW, E-mail), divisions can be specified as one of the search option, and furthermore, in the EST division, organisms can be selected from 21 organisms which are listed based on the submitted-numbers' statistics (this option is effective only when "DDBJ ALL" or "DDBJ updates" is selected).
Silurana tropicalis, one of the 21 EST organisms was merged into Xenopus tropicalis in 2004. But, we missed taking this change into database construction processes, and also did not change the description of the search page. Therefore, X. tropicalis have not been able to be selected as the EST organism, and the search being selected S. tropicalis have not been made properly.
Details are as follows.
  • Period:2004.07. - 2006. 01.20
  • Affected databases:all homology search programs (WWW, E-mail) except for PSI-BLAST
  • Situation:When S. tropicalis of EST was specified as a division, the search did not return the hit no results (Nevertheless, when "select-all" or "others" of EST division was selected, the correct results were obtained.)
  • Correction:database construction program bug was fixed. Descriptions of the search pages and their help pages were revised. Now the correct search results are available. Furthermore, a check program to prevent reoccurrence of similar troubles will be introduced.
 
PRI division data were misclassified as HUM in release 63
The 37 PRI entries (see the list) were included in the HUM division of DDBJ previous release 63 by our mistake. Details are as follows.
  • Corresponding release: DDBJ release 63 (September 2005)
  • Relevant Accession numbers: See the list
  • Measures: These 37 entries are correctly included in the PRI division of DDBJ release 64 (December 2005)
    On getentry and anonymous FTP, the corrected entries have already been available.
  • Affected DDBJ services and period: All services including the following services
    - getentry (early October, 2005 - 2005/12/28)
    - Anonymous FTP (2005/9/30 - 2005/12/28)
    - SRS, ARSA, Homology Search services (early October, 2005 - 2006/02/13)
      *Please note that some services will be affected by this trouble even after release 64 is released, for a short time.
    ==>Correction was completed in all services.(Feb.13, 2006)

Incomplete release of VRL division data The 52 VRL entries were not included in DDBJ periodical releases from 46 to 63 by our mistake. At first, these entries were released as EST data in 2000 and then, they were changed to VRL division for some reasons in 2001. After that, they were not included in DDBJ releases as mentioned.
Details are as follows.  
  • Period in which the entries were not included in DDBJ releases: From DDBJ release 46 (Jul. 2001) to release 63 (Sep. 2005)
  • Relevant Accession numbers: See the list
  • Measures: We reported and apologized to the submitters for our mistake. In the forthcoming DDBJ release 64, these 52 entries will be included in the VRL division data.
  • Affected services: Anonymous FTPs and search/analysis services (exclude getentry*)
    *These entries have been enabled to see by using getentry since their first release. However, in the mean time, they were provided in an old format. These 52 entries data are served now.




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