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 email@example.com. We really want to hear from you!!!!
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.
"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.
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.
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.
Functional Genomic Analysis of E. coli in Japan
GIB Escherichia coli K-12 W3110
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
The recent DDBJ activities were introduced in the special database issue of Nucleic Acids Research Vol.34 Database Issue (Jan. 1).
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.
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.
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.
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.
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.
Last modified: Oct. 07, 2011