DNA Data Bank of Japan
DDBJ Mail Magazine 
No. 21 (October 31, 2005)
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 ♦ Have you ever noticed the face on a USB flash drive? 
face on USB One day, I suddenly felt that someone was looking at me, and found that glance was from my reticence USB. The face had bold eyebrows (almost square) with beady eyes that are watching me. Even more, it had a nose and a mouth..., does't it alike? Please checkthe picture. I have been using this USB flash drive for quite long time without noticing such a face. Just to be sure, I checked other USB flash drive and found that there are holes in all of them, which resemble parts of faces. The functional requirement brought every detail into face-like arrangement. Wow, this must be the ultimate function beauty? not sure.
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!!!!

 ♦ Creation of the ENV division 
Recently, the submissions of the sequences derived from environmental samples have rapidly been increased. To accommodate such submissions, a new division, ENV, has been created. This division contains the sequences obtained via direct molecular isolation such as PCR, DGGE, or any anonymous method. In the past, the sequences derived from environmental samples belonged to taxonomic divisions, mainly BCT.
At DDBJ, the retrofit to transfer relevant entries from taxonomic divisions to the ENV division started in the periodical release 62 (Jun, 2005), and ends by the periodical release 63 (Sep, 2005). Please note that, during this transitional period, some entries to be placed in the ENV division will be found in other divisions.
Reference: Explanation of DDBJ flat file Format [LOCUS]

 ♦ Layout change !! -- getentry web version 
getentry is the data retrieval system provided by DDBJ through web and E-mail services. The interface of "getentry web version" was modified in Jul. 14, as shown below. Please note that there are no changes on the function of the sequence retrival engine. Enjoy the new modifications made.
Upper frame
- The search box to input a key number was changed as follows.:
  Location: moved from "bottom" to the "top".
  Name: The term "Number" was modified to "ID".
- English /Japanese link switch was added
Lower frame
- Table of "Type of ID supported by each database" was updated
- Terms were standardized.
 ♦ DDBJ Rel. 62 Completed 
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public. We completed DDBJ Release 62 in Jun. 30, 2005. DDBJ Release 62 consists of 45,249,444 entries, and the number of bases reached 49,158,155,283. Env division started from this release.
DNA
database
Rel.DateDDBJ
Date
EntriesBases
DDBJ6206/0506/0545,249,44449,158,155,283
Protein
database
Rel.DateDDBJ
Date
SequencesResidues
DAD3207/0507/052,429,195745,907,868
UniProt5.407/0507/052,024,194652,583,887
UniProt/Swiss-Prot47.407/0507/05186,88267,622,695
UniProt/TrEMBL30.407/0507/051,837,312584,961,192
PRF10305/0506/05381,094133,021,483
PDB PDB updates their database once in a week. DDBJ check
and update it every day (as of Aug. 18, 32,072 entries).


 ♦ International bioinformatics training course in Taiwan 
Two international training courses were given in Taiwan at Yang-Ming University in Taipei (July 6-8) and the National Health Research Institute (NHRI) in Hsin Chu (July 11-12) by three Professors from DDBJ. Prof. Yoshio Tateno gave lectures on Molecular Evolution, Prof. Naruya Saitou taught students about Molecular Phylogeny and Dr. Roberto Barrero introduced the services and tools available at DDBJ, with special emphasis in using the SAKURA nucleotide sequence data submission system, sequence retrieval systems (getentry, ARSA and SRS), GTOP and H-Inv DB. The number of attendees to the theoretical lectures were about 20-25 people, while for the practical sessions 10-15 people took part. A new invitation by local researchers was extended to DDBJ professors to make another International Training Course in the near future.
Yan Min Univ NHRI
[Left: Yang-Ming University, Right: NHRI]

 ♦ DDBJ new staff 
Dr. Kenta Sumiyama (Assistant Professor of the Division of Population Genetics, NIG) joined DDBJ. He has been Assistant Professor at NIG since March 2003, and has been working for DDBJ from April this year.
He said that he was hoping to contribute to making better DDBJ interface, with taking an user viewpoint into account.

 ♦ Close notification---SF gate-WAIS and malign 
We are going to stop the services for "SF gate-WAIS" and "malign" at September 30, 2005. The number of users of these tools is on the decrease and we provide other new tools to substitute the above such as SRS or ARSA (keyword retrieval system) and ClustalW (multiple alignmentand tree-making system).
We apologize for any inconvenience that this may cause.

 ♦ URL change: CAMUS Database and SSThread 
CAMUS Database and SS Thread will change operating server and their URL.
Details have not been decided yet, such as the date of change, etc.
However, as soon as details are available, we will notify them at the respective service pages.
- CAMUS Database: Compressed DB for homology searches and multiple-aligned sequence DB.
- SSThread: Prediction of protein secondary structure using threading.



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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
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Last modified: Oct. 07, 2011