DDBJ Web Magazine-e April 2013 Issue Apr. 25, 2013

Latest version    Backnumber    Published by DDBJ

Suspension of some parts of DDBJ activities during Japanese holidays
We at DDBJ will suspend our business on releasing data and answering inquiries from April 27 to 29 and from May 3 to 6, 2013. Search, analysis and other WWW services are available. We will resume the normal business from May 7.
Thank you for your understanding and cooperation.
Enhancement in DDBJ BLAST
DDBJ greatly improved the homology search BLAST.
  • Selections of Data Sets and Divisions were modified
  • Get the result by E-mail, as well as in the web screen
  • Direct link to the flat file of the corresponding accession number
  • Link-up to ClustalW
  • Request ID was not included in the URL of the result
  • New function Result Viewer was equipped

Browsers Information

BLAST web services have been tested with the following browsers and versions. They may not work with older versions.
("*" in the table means the latest version as of April 8, 2013)

  Internet
Explorer
FireFox Chrome Safari
Windows XP ≥ 8.X * * -
Windows 7 ≥ 9.X * * -
Mac OSX10.6 - * * ≥ 5.X
Mac OSX10.8 - * * ≥ 6.X
 

Selections of Data Sets and Divisions were modified

(1) Datasets are selected from DDBJ ALL, DDBJ New, 16SrRNA (in case of nucleotide)
(2) In the specification of Divisions, you can select general classifications (Standard divisions, High throughput divisions, EST divisions, Other divisions), and detailed specification of divisions are available.

 

get the result by E-mail, as well as web screen

You can select the method of getting the result either E-mail or WWW.  

direct link to the flat file of the corresponding accession number

You can view the flatfile of the sequences in the getentry.

 

Request ID was not included in the URL of the result

After pressing the "Send to BLAST" button, Request ID is displayed on the web screen. Don't loose this ID because it is necessary for using the "Result Viewer" and/or inquiring to DDBJ for your search.

 

New function Result Viewer

You can view your result using "Request ID" at any time (within the retention period).

 

Link-up to ClustalW

Select the sequences which you would like to succeed the clustalW, then press the "ClustalW" button. Your selected sequences are automatically pasted in the ClustalW query box.

 

DDBJ will continue to improve the services. Your revise and comments will be helpful for DDBJ's improvement. Please send your comments from "Contact Us" page. (Please select the item "Web Support ")

Release of sequence data from DDBJ (Apr. 2013)
DDBJ released genome sequence data of mouse (Mus musculus strain MSM/Ms), which had been submitted by National Institute of Genetics.

The accession numbers are as follows. They are available on getentry.

    WGS: BAAG010000001-BAAG011237600 (BAAG.gz) (1,237,600 entries)


DDBJ released genome sequence data of a biofuel crop, Jatropha curcas, which had been submitted by the Kazusa DNA Research Institute.
The sequence data are updated version of previously released one.

Reference URL;Jatoropha database

The accession numbers are as follows. They are available on getentry and DRASearch.

    scaffold CON: DF145383-DF157092 (11,710 entries)
    WGS: BABX02000001-BABX02066610 (BABX.gz) (66,610 entries)
    raw data: DRR001794, DRR001795
New COMMENT format for Japan Patent Office (JPO) data
Hideo Aono
DDBJ Patent Annotator



Introduction

DDBJ makes an improvement of COMMENT Block on Flat File (FF) for Japan Patent Office (JPO). In this column, I would like to introduce new format of COMMENT Block in detail.

DDBJ re-constructed FF of all JPO entries to reflect new COMMENT format.
New format of Nucleotide sequence data has been released since DDBJ release 90 (Fig.1) and Amino acid sequence data has been distributed JPO cumulated files on Anonymous FTP since September 2012 (Fig.2).



1. New format of COMMENT Block
JPO data has almost basic information for patent application. Therefore, user can get its information without referring patent publication.
However, since patent information was set on different part of FF, user had to know the FF structure to get them in advance. In specially, applicants name is only set JOURNAL line on REFERENCE Block (Fig.3 & Fig.4).

   Fig.3 Applicant name on REFERENCE Block
   
Therefore, DDBJ made describing basic patent information on COMMENT Block as follows (Fig.4).

   Fig.4 Description of each line on REFERENCE [A] and COMMENT Block [B]
   

COMMENT Block was added new lines of PA (Applicant name), PT (Invention title) and PS (Sequence number) in all nucleotide and amino acid sequence data (Table.1).

   Table.1 New lines of COMMENT Block
New line name Description
PA line Applicant name
JOURNAL line on REFERENCE Block is also described (Fig.3).
PT line Invention title
DEFINITION, TITLE line on REFERENCE Block are also described (Fig.1 & Fig.2).
PS line Sequence number
Sequence number for Sequence listings setting after prefix letter "N".
2. Sequence number
2-1:

There was mismatch problem of Sequence number between Sequence listings and JPO submission file. Old format FF was not described Sequence number of Sequence listings. Therefore, DDBJ added PS line on COMMENT Block to set its number.

2-2:
When applicants applied patent, they made Sequence listings according to the guideline: WIPO ST.25. It was put ordering number from 1 to nucleotide and amino acid sequences based on patent claims by applicants.
On the other hand, JPO changes sequence order and makes nucleotide sequence block and amino acid sequence block from Sequence listings when they make the submission files to DDBJ. After that, they set new Sequence number in order of nucleotide sequences, amino acid sequences (Table.2).

   Table.2 Correspondence of Sequence number between Sequence listings and FF
   

2-3:
Sequence number indicated by JPO is reflected with patent publication number on DEFINITION, KEYWORDS, JOURNAL line of REFERENCE and PN line of COMMENT Block.
Publication of patent applications and Japanese translations of Patent Cooperation Treaty (PCT) international publication for patent applications have same format of publication number with "JP". PCT international publication for patent application has "WO" in head of publication number (Fig.1, Fig.2 and Table.3).

   Table.3 Description part and Format of patent publication on FF
Description part of FF Format of patent publication
DEFINITION
KEYWORDS
PN line of COMMENT Block
JP[space]Patent publication number[-A/]Sequence number
WO[space]Patent publication number[-A/]Sequence number
JOURNAL line of REFERENCE Block JP[space]Patent publication number[-A][space]Sequence number
WO[space]Patent publication number[-A][space]Sequence number
2-4:
Sequence number Sequence listings are set after prefix letter "N" on PS line. Therefore, you can retrieve appropriate data by ARSA (All-Retrieval of Sequence and Annotation) with publication number and "N" with Sequence number.

Author comments
DDBJ continues to make an improvement of Patent FF for user. As next step, we are planning FF put on direct link of the patent publication.
“FAQ of DDBJ Nucleotide Sequence Submission System” –Vol.2
FAQ about New DDBJ Nucleotide Sequence Submission System.


Q1.At page "7. Annotation", I got an error message saying ‘First codon [aac] is not a start codon. / Final codon [atg] is not a stop codon.‘ What should I do?

A.. This message occurs when the protein-coding sequence is not complete. Please add "<" and/or ">" marks to the location according to the rule for description of location.


     Reference: Description of Location


Q2.At page "7. Annotation", I got an error message saying ‘To use [translation] qualifier, [exception] qualifier is required in the [CDS] feature. ‘ What should I do?

A.This error message comes out when you chose only "/translation" qualifier at CDS feature. Usually, you do not need to add "/translation" qualifier to CDS feature, therefore, please remove it from the CDS feature.
Both /exception and /translation are used at CDS only when actual amino acid sequence is not the same with the translation obtained from DNA sequene due to RNA editing, rearrangement, or translation from the corresponding transcript or proteomic data.

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

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