DNA Data Bank of Japan
DDBJ Mail Magazine 
April.18, 2006
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 ♦ Life without flowers is just totally pointless.  
full of cherry blossom This is the web version of the bimonthly DDBJ Mail Magazine (Number 25th).
Do you enjoy the upcoming season? In NIG, we really have been enjoying beautiful cherry blossom seasons. This scene makes us feel the begining of new period...

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 DDBJing 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 June 14-15, "The 15th DDBJing" will be held in Mishima at the National Institute of Genetics. This upcoming course is aimed especially for begginers. However, we are sure to welcome the repeater of DDBJ services because we have some changes of our services. The program of this DDBJing is oriented towards the use of sequence submission facilities and also revises the use of Search & Analysis tools.
We will announce the details at our HP top page and at the DDBJing site.
If you have interest, we will welcome your participation. However, please note that most of the DDBJing lecture will be in Japanese.

 ♦ New functions were added to "getentry" web server 
"getentry" is the sequence retrieval system provided by DDBJ via WWW and E-mail servers. Entries can be retrieved using various types of "key words" or "sequence identifiers" such as Accession Numbers.
In the getentry web server, there are 3 ways to obtain the results of sequence retrieval, namely: interactively, by E-mail, or by anonymous FTP. In case you select "anonymous FTP", up to 100,000 entries can be downloaded as anonymous FTP by clicking the file name shown on the screen. Notice that it makes you take long time to generate the result for anonymous FTP, especially in the case of large-size files. Until recently, the status of the file generation process for anonymous FTP could not be visualized with the inconvenience of not being able to tract the retrieval process.
To solve this need as of March 13, 2006, two new functions were implemented in the generation of anonymous FTP results.

 1. "File making progress check"
Please click on "the state of making the file" in the lower frame part to visualize the status of the file making process.
 2. "Completion e-mail notification"
An e-mail notification will be sent to the user after completion of the generation of the result file for anonymous FTP. Users need to enter a contact e-mail address.

Both features are useful when you use anonymous FTP to obtain the getentry retrieval results.
Please note that the completed result file will be deleted automatically after 24 hours of notification.

*Because of the temporal system error, the search results available in anonymous FTP were limited up to 5,000 entries. This trouble was fixed on March 13.

 ♦ Functional improvement of BLAST at web server 
DDBJ provides BLAST (Homology Searching service) from its "web", "SOAP", and "E-mail" servers.
Graphical View is the function of BLAST at web server that displays the results as graphics and simplifies the linkage to ClustalW.
DDBJ has expanded the function of BLAST to facilitate the handling and processing of results. Now, after the homology screen is completed, users can select the threshold of E-value/Score and/or the range of overlapping region of sequences similar to the "query" to conduct ClustalW analysis. The new changes were implemented on February 2nd. The details are as follows:

Expansion of the Result Viewer page
Concerning the "Graphical View" and "Text View" formats of the result viewer page, we enabled to select option (1) and/or (2), as described below, by selecting either "AND" or "OR" operators.
  (1) E Value or Score
Select either "E-Value" or "Score" and then input a (threshold) value. Press SELECT button to retrieve all sequences fulfilling the condition.
  (2) Overlapping Positions
Specify the position of query and select "Entirely" or "Partially", and press SELECT button to retrieve sequences fulfilling the condition. [Entirely: include entire range that was inout. Partially: include part of the input range. If you input only one text box, sequences including the input position are selected.]
In addition, it is also possible to specify "AND" or "OR" for specifying a combined condition of E Value/Score and the Overlapping Positions.
When only one of the two options is used, both of the specification of "AND" and "OR" selects the same sequences.

Modification of the functional connection with ClustalW
When you search with blastx or tblastx and connect to the ClustalW with the selection of your Query and hitted entries, it combines DNA entries and Amino Acid entries. To avoid this, when either blastx or tblastx is selected, you cannot specify the Query.

We place a "GO TO CLUSTALW" button on top and bottom of the page to facilitate the analysis.

 ♦ The distribution of massive entries 
The mass sequence data which were collected by DDBJ and release through the INSD (International Nucleotide Sequence Database) from this January to March are as follows;

Release of new 136 thousand Human EST entries
DDBJ newly released 136 thousand Human EST entries, which had been submitted by RIKEN Genomic Sciences Center. The accession numbers are as follows; DB441779-DB577968 (136190 entries) These entries were released as DDBJ daily updates on March 14.
All of the data can be retrieved at anonymous FTP site.
  - Homo_sapiens_EST_20060314_1.seq.gz

Release of new 780 thousand Rice EST entries
DDBJ newly released 780 thousand Rice (Oryza sativa (japonica cultivar-group)) EST entries, which had been submitted by the National Institute of Agrobiological Sciences. The accession numbers are as follows;
  * CI000001-CI778739
These entries were released as DDBJ daily updates from Jan. 31 to Feb. 2. All of the data can be retrieved at anonymous FTP site.
  - rice_EST1.seq.gz (CI000001-CI250000, 83MB)
  - rice_EST2.seq.gz (CI250001-CI500000, 76MB)
  - rice_EST3.seq.gz (CI500001-CI778739, 79MB)

Update of 1.6 million Human EST entries
DDBJ updated 1.6 million Human EST entries on their reference information by the request for "The Institute of Medical Science The University of Tokyo" and "Reverse Proteomics Research Institute Co.,Ltd". The accession numbers for these entries are as follows;
  * AU116789-AU117215
  * AU117217-AU144110
  * AU144112-AU160826
  * AU279383-AU280837
  * BP192706-BP383670
  * DA000001-DA999999
  * DB000001-DB384947
These entries were released as DDBJ daily updates from Jan 17 to 26.
All of the data can be retrieved, displayed and acquired by using the DDBJ retrieval tool, getentry.

 ♦ General Terms and Disclaimers for DDBJ users 
We have opened [Goriyouno maeni (Japanese title)] page at our HP on March 28.
In this page, we introduce the directions about the usage of DDBJ services for the DDBJ users. This page states the "Right and Duty concerning to Submission", "Directions for the data usage",. "Site Policy", and "Secure Personal Information Management". You can see this page by clicking the 2nd button from the top at left column. [we apologize that this page is currently only in Japanese.]

 ♦ The report of Japan-Korea-China Bioinformatics Training Course 
DDBJ successfuly held the Japan-Korea-China Bioinformatics Training Course from March 14 to 17 at NIG.
The 31 young reserchers (11 from Japan, 10 from Korea, and 10 from China) and observers were given lectures and trained from 8 in the morning to 7:30 in the evening for 4 days. All lectures were given in English. On this occasion, besides the Japanese, Korean, and Chinese instructors, we invited lecturers from Singapore, Thailand, and Indonesia.
We schedule to hold the next Bioinformatics Training Course in 2007. As soon as the details are decided, we will announce at DDBJ HP and DDBJ Mail Magazine. If you have interest, please check our website frequently. The picture is about the lecture scene.

 ♦ Termination of the "S&W SEARCH" service 
As we had announced at the DDBJ HP (Mar. 9, 2005), the homology screen S&W SEARCH service, provided through web and e-mail server by DDBJ, was terminated due to a failure in the hardware system.
The original company that developed the hardware of S&W SEARCH has been dissolved, which makes difficult the maintenance of the system. From March 22nd the S&W SEARCH service was unavailable, and we tried to in-house repair it. Nevertheless, it was not possible to achieve the same quality of service after the reparation was made. Thus, we decided to terminate the S&W SEARCH service on April 7th.
DDBJ also provides another algorithm SSEARCH, which has a similar function and service to S&W SEARCH, and this service is continuously available.
We thank you for your understanding and cooperation.

 ♦ Termination of DDBJ/CIB Human Genomics Studio by DDBJ 
As we have preliminarily announced, DDBJ/CIB Human Genomics Studio service provided through web server by DDBJ was terminated on March 31, 2006, because of a hardware malfunction.
The H-Invitational Database CIB-DDBJ Flat File Server contains not only all the information provided by the DDBJ/CIB Human Genomics Studio, but also other useful information related to gene function, gene expression, disease association and evolution. Thus, this database will provide updated information related to human genes and their gene products.
We appreciate for your understanding and cooperation.

 ♦ ERRATA Page 
DDBJ have been paying heed to the construction of databases and the various services provided. Neverthless, there were some troubles from February to March (listed below). At present, such problems have been corrected. We apologize for the inconveniences caused to our users.
We recently established a [ERRATA] page at DDBJ HP that can be accessed from the Top page right column. The recovery of the system will be announced on this page as soon as the repairing works are finished. We are working out measures to prevent recurrences of such troubles.

Keyword search results error on SRS "AUTHORS" and "TITLE" fields
SRS is one of the keyword search services provided through web server by DDBJ. Some failures were found in index files. If you used SRS during the affected period (see below) specifying "DDBJRELEASE" as the target database, a part of the "AUTHORS" and "TITLE" fields were not searched. Therefore the result delivered to you might not be complete. Now, the service is available without any problem.
The details are as follows.

* Affected database and search field
    In "Quick Search" : DDBJRELEASE were selected as the Sequence libraries to screen.
    In "Advanced Search" : DDBJRELEASE and/or DDBJ were selected as the Sequence libraries, and any one (or more) of "AllText", "Authors", and "Title" was/were specified as search field
* Affected period:
In "AllText" field :
    In "Authors" field: October 2004 - March 13, 2006
    In "Title" field: February 2006 - March 13, 2006
* Measure: Index files revisions to solve the problem were completed on March 13, 2006

System failure on Homology search services
Some system failures were found in DDBJ's homology search services. If you used DDBJ's homology search services during the following period (see below), your search result might not be correct.
The details are as follows.

* Affected period : February 19, 2006 - February 27, 2006
* Affected services :all homology search programs (WWW, E-mail) except for PSI-BLAST
* Affected database : nucleotide sequence database
* Affected divisions : BCT (bacteria)
     GSS (genome survey sequences)
     MAM(mammals other than primates and rodents)
     PLN (plants)
     SYN(synthetic DNAs)
     VRT(vertebrates other than mammals)

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