DNA Data Bank of Japan
DDBJ Mail Magazine 
May 22, 2007
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 ♦ The summer day. 
It has been very hot these days as May. One day, the temperature went upto over 30 centigrade in the part of Shizuoka prefecture. One of my coworker heard the sound of cicada!!
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!!!

 ♦ New system 
It has been two years since the 1st committee of supercomputer system specification on February 3, 2005. National Institute of Genetics(NIG) has started the new supercomputer system on February 27, 2007. Therefore many kinds of data processing in DNA Data Bank of Japan(DDBJ) became faster to high degree.
It became faster as follows in the case of data management and data publishing process.
Creation of mass flat file: Increase from 300,000 entries to 1 million entries during one night. Creation of huge flat file: Shorten from 1 hour and 50 minutes to 13 minutes for four rice chromosome entries. Creation of live list*1: Shorten from 1 hour and 40 minutes to 13 minutes. Mass EST processing: From 30,000 - 40,000 entries to 500,000 - 800,000 entries per hour. It became faster 15 - 20 times.
The speed improvement was achieved by changing to distributed database and the improvement of the application to make use of the database.

Homology search also became faster. (performance ratio with the old system):
BLAST became 7.71 times, PSI-BLAST 7.89 times, FASTA 4.73 times, SSEARCH 5.55 times and CLUSTALW 7.94 times. The speed improvement was achieved by the number of clocks having gone up and the operation of each application was improved. In addition, also number of cores of CPU*2 increased from 176 to 256 by 1.45 times and the receivable number also increased. The efficiency of the other data processing is also improved. Therefore you are able to use DDBJ comfortably.

Well, we made the contract to strengthen the computer system in 2008 evaluating the latest equipment at that time. Therefore the product obsolescence of the end of the rental period that is common worry about the large-scale computer center is expected to be able to be avoided somewhat. However, the major premises of the specification which is designed from 2005 to 2006 may become useless by the evolution of new research such as development of new sequencer and meta genome analysis*3.
  • *1 live list: Whole published data list which is used to avoid conflict of published data among 3 centers. The data is exchanged between Genbank and EMBL.
  • *2 number of cores of CPU: A conventional PC has one CPU which has a core (single core). It executes two or more applications on the core simultaneously by running in detail. The recent PC has another CPU which has two cores. If it says simply, two kinds of applications can be executed in each core of dual core CPU. Therefore the application may complete at half time compared to using single core CPU. A CPU with four cores begins to be used in PC clusters.
  • *3 recent case: The data derived from Global Ocean Survey project. It is 4 million contigs (AACY020000001-AACY024124495) which has more than 6 million protein annotations.


 ♦ The announcement of DDBJing short training course. 
DDBJing course 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 course, 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 May 29-30, "The 17th DDBJing course" will be held in Mishima at the National Institute of Genetics. This upcoming course is aimed especially for beginners. However, we are sure to welcome the repeater of DDBJ services because we have some changes of our services according to the computer replacement. The program of this DDBJing course is oriented towards the use of sequence submission facilities and also revises the use of Search & Analysis tools.

 ♦The distribution of massive entries  
DDBJ newly released tammar wallaby (Macropus eugenii) GSS 147,312 entries, which had been submitted by RIKEN Genomic Sciences Center. These entries were released as DDBJ daily updates on Mar. 10.


 ♦ Full-length cDNA sequening of brain-expressed gene of cynomolgus monkey in PLOS Biology 
Full-length cDNA sequening of brain-expressed gene of a cynomolgus monkey, Macaca fasciculariswas reported in PLOS Biology, and appeared in January as an online version.
In this paper, full-length cDNA sequencing on the brain transcriptome of an Old World monkey (OWM) was carried out, and then conducted comparative analysis among human, OWM, chimpanzee, and mouse. Authors belongs to the reserach institute and/or university in Japan, Taiwan, and USA. Dr. Takashi Gojobori, director of Center for Information Biology and DNA Data Bank of Japan(CIB-DDBJ), is one of the authors.
Brains of higher primates have evolved rapidly, whereas brain-expressed genes are known to evolve slowly in mammals. In human, there are a lot of questions between the rate of evolution of brain-expressed genes and evolution of the brain itself. To clear this questions, comparative study of the variation of the DNA sequences of various species is necessary.
The data was submitted to DDBJ/EMBL/GenBank International Nucleotide Sequence Databases and was released under the Accession numbers AB170063 - AB174733. The sequence information is available via DDBJ anonymous FTP (whole data download) or getentry system.

 
Genome data were added to GIB Feb. 19, 2007
GIB (Genome Information Broker) provides an integrated search of Bacteria, Archaea, Eukaryota complete genome sequences.
Because the following genome sequence data were released from January 26 to February 19, 2007, we incorporated them to GIB, and now you can search those data.
  • Methylibium petroleiphilum PM1 (by Joint Genome Institute)
  • Lactococcus lactis subsp. cremoris MG1363 (by Bielefeld University)
  • Methanocorpusculum labreanum Z (by Joint Genome Institute)
  • Burkholderia mallei NCTC 10229 (by The Institute for Genomic Research)
  • Streptococcus pyogenes Manfredo (by Sanger Institute)


 ♦ The 6th Japan-Korea-China Bioinformatics Training Course 
From Mar.27 to 30, the 6th Japan-Korea-China Bioinformatics Training Course was held at Shanghai Jiaotong University, Shanghai, China.
From Japan, there were 10 attendees with the Korean and Chinese researchers of Bioinformatics filed and had lectured and joined practical works in English. This training course was targeted to the young Japanese, Korean and Chinese researchers, and also purposed to be used as the social exchange.
From DDBJ, Prof. Gojobori, Prof.Tateno and Prof. Saitou had served as the lecturers.

 ♦ Staff transfer 
CIB-DDBJ had big personnel transfer.
First, the Director of CIB was changed from Prof. Gojobori(Professor of Laboratory for DNA Data Analysis) to Prof. Sugawara(Professor of Laboratory for Research and Development of Biological Databases). This is because Prof. Gojobori was appointed as the Vice President of National Institute of Genetics.
Prof. Nishikawa(CIB-DDBJ Laboratory for Gene-Product Informatics) was retired at March 31th.
As the chief of the System Management Department, he managed to the system management of NIG and coped with the SPAM mail problems.
He left for Maebashi Institute of Technology.
Dr.Abe(Assistant Professor of the Laboratory for Research and Development of Biological Databases) was also left his position at March 31th. Since April of 2004, he had been working for DDBJ and had great contribution to system operation and this years’ system replacement.
He left for his new position at Nagahama Institute of Bio-Science and Technology.
We wish them continued success and happiness in the future.

 ♦ System error 
Link Error in the homology search results display
In the homology search services which DDBJ provide via WWW and by E-mail, we found there had been link errors in the results display. Details are as follows.
*Services: BLAST, FASTA, PSI-BLAST, SSEARCH
*Period: February 27, 2007 - March 17, 2007 11:00
*Cconditions:
  • In the result view screen。、because LOCUS name had been mislocated in the position of accession numbers,(see below)
  • When you check your results in Result Viewer, if you did the search during the above peiord, there are the same error.
*Result The search Result is correct.
---------------------------------------------------------------------
                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AAU58946|U58946.1 Aspergillus awamori transposable element Tan1,...   3979  0.0  
    (Above is the Locus name, and "link" did not work correctly)
AM270150|AM270150.1 Aspergillus niger contig An07c0330, complete...   3866  0.0  
AM270394|AM270394.1 Aspergillus niger contig An18c0010, complete...    517  e-143
AM270353|AM270353.1 Aspergillus niger contig An16c0010, complete...    517  e-143
---------------------------------------------------------------------
*Measure The databases for homology searches was reconstructed. (Reconstruction works had already been completed on March 17.)
Now the service works normally. We apologize for your inconvenience.

Apology for not updated of Anonymous FTP - TPA and CON - (INSD-XML) in DDBJ Rel. 68
In DDBJ release 68, the Anonymous FTP about TPA and CON of the INSD-XML was not updated. Please acquire the data again, if you got the data for the following period.
Thank you for your cooperation and understanding.


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