Don't you feel that we have been in the strange season because of this unsettled temperature? Please be careful of your health!
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 computer system in the National Institute of Genetics was replaced in this March. According this replacement, there are some WWW services whose URLs are changed. Please update your links to new URLs. Presently, both new and old URLs are accessible for a while, however, eventually, old URLs will be stopped.

 

Name	Current URL
	New URL
TXSearch	http://sakura.ddbj.nig.ac.jp/uniTax.html
	http://txsearch.ddbj.nig.ac.jp/
PDB Retriever	http://www.ddbj.nig.ac.jp/search/
	http://pdbret.ddbj.nig.ac.jp/
SSThread	terminate as of 2007/2/23
CAMUS	terminate as of 2007/2/23
Lib score	http://hypernig.nig.ac.jp/cgi-bin/Lib-score/
	http://libscore.ddbj.nig.ac.jp/
Search & Analysis	http://www.ddbj.nig.ac.jp/search/Welcome-e.html
	http://www.ddbj.nig.ac.jp/search/top-e.html
FASTA	http://www.ddbj.nig.ac.jp/search/fasta-e.html
	http://fasta.ddbj.nig.ac.jp/
BLAST	http://www.ddbj.nig.ac.jp/search/blast-e.html
	http://blast.ddbj.nig.ac.jp/
PSI-BLAST	http://www.ddbj.nig.ac.jp/search/psi_blast-e.html
	http://psiblast.ddbj.nig.ac.jp/
SSEARCH	http://www.ddbj.nig.ac.jp/search/ssearch-e.html
	http://ssearch.ddbj.nig.ac.jp/
ClustalW	http://www.ddbj.nig.ac.jp/search/clustalw-e.html
	http://clustalw.ddbj.nig.ac.jp/
hmmpfam	New service
	http://hmmpfam.ddbj.nig.ac.jp/
LIBRA	http://www.ddbj.nig.ac.jp/search/
	http://libra.ddbj.nig.ac.jp/

The system will be switched in the late in February. It might difficult to access DDBJ HP and WWW services during 10days after switching to the new system. In such a case, please try to access again after a while.
Thank you for your understanding and cooperation.

DDBJ newly released two databases, Genome Information Broker for Viruses (GIB-V) and Gene Trek in Procaryote Space (GTPS).
Genome Information Broker for Viruses (GIB-V)
Genome Information Broker for Viruses (GIB-V) is a complete virus genome data repository.
URL: http://gib-v.genes.nig.ac.jp/

Gene Trek in Procaryote Space (GTPS)
"GTPS" is acronym of Gene Trek in Procaryote Space. Various complete genomes of eubacteria and archaea have been registered in the International Nucleotide Sequence Databases (INSD) of DDBJ/EMBL/GenBank. URL: http://gtps.ddbj.nig.ac.jp/

"DDBJ working on evaluation and classification of bacterial genes in INSDC"
Hideaki Sugawara, Takashi Abe, Takashi Gojobori and Yoshio Tateno
"DDBJ working on evaluation and classification of bacterial genes in INSDC" Hideaki Sugawara, Takashi Abe, Takashi Gojobori and Yoshio Tateno
Nucleic Acids Research, 2007, Vol. 35, Database issue D13-D15
(Summary) DDBJ newly collected and released nucleotide sequence data containing honeybee expressed sequence tags (ESTs), re-examined and re-annotated complete genome data of Escherichia coli K-12 W3110, medaka WGS and human MGA, in the period from July 2005 to June 2006. DDBJ also systematically evaluated and classified the genes in the complete bacterial genomes submitted to INSDC. (PMID: 17108353)

OMICS 2006 (about TPA)

"Evidence Standards in Experimental and Inferential INSDC Third Party Annotation Data"
Guy Cochrane, Kirsty Bates, Rolf Apweiler, Yoshio Tateno, Jun Mashima, Takehide Kosuge, Ilene Karsch Mizrachi, Susan Schafer, Michael Fetchko
OMICS 2006, Vol. 10, No. 2: 105-113
(Summary) The analysis of increasing TPA(Third Party Annotation) submission case-study was co-written by three international databases: DDBJ, EMBL, GenBank.

DNA Research (about GTPS)

"Exploration and Grading of Possible Genes from 183 Bacterial Strains by a Common Protocol to Identification of NewGenes: Gene Trek in Prokaryote Space (GTPS)"
Takehide Kosuge, Takashi Abe, Toshihisa Okido, Naoto Tanaka, Masaki Hirahata, Yutaka Maruyama, Jun Mashima, Aki Tomiki, Motoyoshi Kurokawa, Ryutaro Himeno, Satoshi Fukuchi, Satoru Miyazaki, Takashi Gojobori, Yoshio Tateno, and Hideaki Sugawara
DNA Research Advance Access published online on December 13, 2006
(Summary) please refer to the address above

DDBJ provides ClustalW services through WWW and E-mail. The DOTSINOUTPUT option(The marched characters of the alignment are displayed by the dots) is available for ALIGNMENT, but unavailable together with the "TREE" and/or "BOOTSTRAP" options. DOTSINOUTPUT option is the DDBJ's original options in the ClustalW.

CLUSTAL W (1.83) multiple sequence alignment query MDMEIEDSSPIDDLKLQKLDTNVYFGPCEILTQPILLQYENIKFIIGVNLSTEK P39728-1 ...................................................... Q759A6-1 -------M.Q.QP.Q.SA..F...LNT.S.AEFIESK..R.F.SIGIPIQ.VVE Q6FV15-1 -------------.Q..S.IF..SLAT..E.HT..QR..R.F...GI.NHVF.N Q12182-1 -------------.R..NHIF..SVHS..HTDF.VEN..R.F.N.D....L.SH Q6CIX1-1 -------LNQM.P.Q.SN..F...LNT.S.YDF.SKND...F.S.GIPV.R--- *:*. :::**. *:. : .:*:*:*.:.:. .

DDBJ provides homology search services by WWW and E-mail. "16S rRNA" is newly added to the searchable databases in FASTA, BLAST, and SSESRCH services. Details are as follows.

• Database: 16S rRNA (Prokaryotes)
• method:
  1. The 16S rRNA sequences which meets the following conditions were extracted from BCT division of the latest DDBJ periodical release.
     
     • include "rRNA" in Feature Key
     • include 16S", "RRS" or "SSU" in the product line of Qulifier Key.
  2. After extraction, the sequences whose length is 300bp or less and which ar recognized as the antisense were removed.
• Anonymous FTP:
  
  • File Name : 16S.seq.gz (FASTA format)
    
  • This data is also available from "Anonymous FTP of the DDBJ".

DDBJ upgraded BLAST (provided through WWW and E-mail) and PSI-BLAST (WWW only), which are DDBJ's homology search services, from 2.2.14 to 2.2.15. The upgraded services correspond to the retrieval of the amino acid including "J" and "O"

The massive sequence data which were collected by DDBJ and released through the INSD (International Nucleotide Sequence Database) from this October to November are as follows:

 

Release of new Medaka GSS 430,750 entries Dec.27, 2006

DDBJ newly released Medaka (Oryzias latipes, strain Hd-rR) GSS 430,750 entries, which had been submitted by National Institute of Genetics. These entries were released as DDBJ daily updates on Dec. 22, 23 and 26.

Reference URL: http://dolphin.lab.nig.ac.jp

Accession numbers: DH000001-DH430750 (430,750 entries)

anonymous FTP: Oryzias_latipes_GSS_061222_1.seq.gz

 

Correction for the "Release of new Xenopus laevis EST 129,076 entries" Dec. 18 2006

In the "Release of new Xenopus laevis EST 129,076 entries (Dec.6)", the description of the organism name was corrected in some data. Details are as follows. For the Anonymous FTP, the new file which contains the corrected data was placed on the following site.
Please download the files again, and replace with the old ones.

• Organism name
  (Error) Xenopus laevis  ---> (Correct) Xenopus tropicalis
  DC135518-DC165593 (30076 entries)
  DC165594-DC195410 (29817 entries)
  
• Correction for the developmental stage description
  (Error) stage 10.5 --->
  (Correct) mixture of equivalent stages 10.5-15 (early gastrula to mid neurula)
  DC066335-DC099907 (33573 entries)
  DC099908-DC135517 (35610 entries)
  
• Anonymous FTP:
  

  Xenopus tropicalis EST
  (file name)	Xenopus_tropicalis_EST_061215_1.seq.gz
  	Xenopus_laevis_EST_061215_2.seq.gz
  Xenopus laevis EST
  (file name)	Xenopus_laevis_EST_061215_1.seq.gz
  	Xenopus_laevis_EST_061215_2.seq.gz

We apologize for your inconvenience.

 

Release of new Xenopus laevis EST 66,334 entries Dec.5, 2006

DDBJ newly released African clawed frog (Xenopus laevis) EST 66,334 entries, which had been submitted by University of Tokyo.

These entries were released as DDBJ daily updates on Dec. 2.

Reference URL: http://www.shigen.nig.ac.jp/xenopus/top.jsp

Accession numbers: DC000001-DC066334 (66,334 entries)

anonymous FTP: Xenopus_laevis_EST_061202_1.seq.gz

 

The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public. We completed DDBJ Release 68 in Dec. 28, 2006. DDBJ Release 68 consists of 64,267,978 entries, and the number of bases reached 68,259,314,742. We changed the maximum file size from 300 MB to 1.5 GB
FTP site for periodical release and new data download  

DDBJ released the new statistics called [Journal ranking 100] from Rel.65.
These statistics are extracted and made up from the journal information in DDBJ release flat file. [by entries] shows the ranking of the number of entries in each journals and [by papers] shows the order of cited frequency of the papers.
(Actually, the way of writing journal name is different from each submitters, however, DDBJ standardize the journal name so that there are no leakage.)

• The number of journals:
  http://www.ddbj.nig.ac.jp/breakdown_stats/journal-num.html
• The number of entries:
  http://www.ddbj.nig.ac.jp/breakdown_stats/journal-ent.html

These statisitics are very unique to DDBJ. The acquisition of INSD's accession numbers are increasingly recognized as the essentials for submission for papers to scientific journals. This journal ranking statistics may be useful as the reference before the submissions.

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