DDBJ Web Magazine-e No.73 & 74


No. 73 & 74   Oct. 23, 2012
Latest version    Backnumber    Published by DDBJ

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New DDBJ Nucleotide Sequence Submission System
A new DDBJ Nucleotide Sequence Submission System has been released on October 3, 2012.
This system has much more effective interface to input annotation than SAKURA. We also revise the error check function. The new submission system is equipped with "jParser", which is also used in Mass Submission System (MSS).

You can download HELP file of the submission system(PDF).
Submission through "SAKURA" will be terminated on October 31, 2012 at 17:00(JST). Please check the following notes.
Notes about SAKURA
  • Data of saved entries and templates, whose submission is in progress, are not transferred into the new submission system.
  • Please complete your submission prior to the termination of SAKURA.
DDBJ Rel. 90.1，DAD Rel. 60.1 released
DDBJ Rel. 90.1 and DAD Rel.60.1 were released, because some disorders were found in DDBJ Rel. 90.0，Rel.60.0 (released on Sep. 2012).

Reference: Apologies for defects in DDBJ and DAD data
The Report for the 25th International Collaborators Meeting
International Nucleotide Sequence Database Collaboration (INSDC), consisted of DDBJ, EBI and NCBI, hold the international collaborators meeting every year.
In 2012, the meeting was held at NCBI in USA, 11-13 June, to discuss practical matters to maintain and update nucleotide sequence data archives; DDBJ, EMBL-Bank, GenBank, Sequence Read Archive (SRA) and Trace Archive.
The outcomes of the meeting are summarized here.
Additional new lines on COMMENT for Japan Paten Office (JPO) data
COMMENT part was added new lines of PA, PT and PS in all nucleotide and amino acid sequence data of Japan Paten Office (JPO).


[Additional lines]
PA: Applicant name
PT: Invention title
PS: Sequence number indicated by applicant

DDBJ constructed FF of all JPO entries to reflect new COMMENT and released them in DDBJ release 90 and JPO cumulated amino acid data files.

[Example]
COMMENT    OS   human
           PN   JP 2010599999-A/100
           PD   29-SEP-2010
           PF   20-NOV-2006 JP 2008583186
           PR   15-MAR-2003 US 60/525115
           PA   DNA Data Bank of Japan
           PI   hanako mishima,taro iden
           PT   "Genetic Markers Expressed In Tumors"
           PS   N55
           CC   genetic maker for genetic diagnosis
           FH   Key Location/Qualifiers
           FT   misc_feature    1..88
           FT   /note="genetic maker"

[DDBJ FTP site]
Please get JPO data from following site.

JPO Nucleotide sequence data:
ftp://ftp.ddbj.nig.ac.jp/ddbj_database/ddbj/

JPO Amino acid sequence data:
ftp://ftp.ddbj.nig.ac.jp/ddbj_database/patent/
"DDBJ Original version" was added to the ClustalW
ClustalW is a general purpose multiple sequence alignment program for DNA or proteins.
DDBJ added DDBJ Original version (Version 1.83, Modified by Dr. Kirill Kryukov) options of the ClustalW.

In the "Version 1.83", you can specify the detailed option parameters for Tree calculation and Bootstrap.
Please refer to ClustalW HELP "DDBJ Original version (Version 1.83, Modified by Dr. Kirill Kryukov) options" for details.
Release of sequence data from DDBJ (Aug. – Oct. 2012)
DDBJ released genome sequence data derived from coelacanth (Latimeria chalumnae), which had been submitted by Tokyo Institute of Technology.

The accession numbers are as follows;(Available by getentry and DRASearch)
  • scaffold CON: DF158906-DF196766 (37,861 entries)
  • WGS: BAHO01000001-BAHO01475424 (BAHO.gz) (475,424 entries)
  • raw data: DRA000580 (DRR002180-DRR002183), DRA000594 (DRR002285-DRR002287)
DDBJ newly released genome sequence data derived from Theileria orientalis strain Shintoku, which had been submitted by Hokkaido University.

The accession numbers are as follows.
  • chromosomes : AP011946-AP011949 (4 entries)
  • apicoplast : AP011950
  • mitochondrion : AP011951

DDBJ released TSA data derived from great pond snail (Lymnaea stagnalis), which had been submitted by Tokushima Bunri University.

The accession numbers are as follows.
  • TSA : FX180119 - FX296473 (116,355 entries)
  • raw data : DRR002012

Published by:
DNA Data Bank of Japan (DDBJ)
DDBJ Center
National Institute of Genetics
Research Organization of Information and Systems
1111 Yata, Mishima, Shizuoka 411-8540, JAPAN

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