DNA Data Bank of Japan
DDBJ Mail Magazine 
Aug.28, 2006
Japanese
   
top Latest version top
backnumber Back number
ddbj Published by DDBJ
This page is translated from Japanese version. Sending "E-mail magazine" has not started yet.
Search for
Site Map
about DDBJ
Data Submission
SAKURA
       Mass Sub
Data Updates
Search and Analysis
ARSA   getentry
TXSearch  
FASTA   BLAST
SSEARCH
  HMMPFAM
ClustalW
 
WebAPI
 
GIB
  GIB-V
GTPS
  GTOP
Breakdown Stats
Download data
  DDBJ Release Note
  Release Information
Q and A
Dorrs for Infomation Bioligy
  Conference on Info Bio

 Contact Us  
Copyright © 1995-2006
DDBJ All rights reserved.
 ♦ The voice of the cicada 
In Japan, we have customs to enjoy the seasonal living things' sounds such as the voice of Japanese nightingales in Spring, cicadas in Summer, pine crickets and bell crickets in Autumn,...etc,. I guess this customs derive from our distinctive four seasons.
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!!!

 ♦ Upgrade of Search and Analysis services 
DDBJ upgrades the Search and Analysis services (FASTA, BLAST, PSI-BLAST, SSEARCH) provided via WWW and E-mail. There are also some change of the screen lay-out and we have added the support of Safari browser.
The datails are as follows;
1 : Upgrade of search program

Service  Before Ver.up    After Ver.up
FASTA   34t21  -> 34t25
BLAST   2.2.12  -> 2.2.14
PSI-BLAST   2.2.12  -> 2.2.14
SSEARCH   34t21 -> 34t25

2 : The change of retrieval result notation
Along with this upgrade, we change the result notation of FASTA and SSEARCH from ungapped notation to similar notation.
format before upgrade
>>sp|P94604|GYRB_CLOAB DNA gyrase subunit B (EC 5.99.1.3  (637 aa)
 initn: 178 init1: 116 opt: 185  Z-score: 272.1  bits: 57.1 E(): 5.2e-08
Smith-Waterman score: 185;  55.932% identity (61.111% ungapped) in 59 aa 
overlap (1-58:167-221)

                                             10        20        30
query                                TTTHFVPDPEIFTETIEFDYDTLANRVREL
                                     :  .: :::::: .: :.:::::..:.:::
sp|P94 KTEGHIWKQTYHRGKVASPFEKIGDSDEHGTKIYFKPDPEIFEDT-EYDYDTLSQRLREL
        140       150       160       170       180        190

               40        50
query  AFLTKGVNIIIEDLREGKERKNE-YCYEG
       :::.::..: . : :.    ::: . :::
sp|P94 AFLNKGIKIELTDERHD---KNEIFHYEGGLKSFVSYLNRNKEVVFKEPIYVEGSIDSNY
         200       210          220       230       240       250

format after upgrade >>sp|P94604|GYRB_CLOAB DNA gyrase subunit B (EC 5.99.1.3 (637 aa) initn: 178 init1: 116 opt: 185 Z-score: 271.6 bits: 57.0 E(): 5.5e-08 Smith-Waterman score: 185; 55.932% identity (76.271% similar) in 59 aa overlap (1-58:167-221) 10 20 30 query TTTHFVPDPEIFTETIEFDYDTLANRVREL : .: :::::: .: :.:::::..:.::: sp|P94 KTEGHIWKQTYHRGKVASPFEKIGDSDEHGTKIYFKPDPEIFEDT-EYDYDTLSQRLREL 140 150 160 170 180 190 40 50 query AFLTKGVNIIIEDLREGKERKNE-YCYEG :::.::..: . : :. ::: . ::: sp|P94 AFLNKGIKIELTDERHD---KNEIFHYEGGLKSFVSYLNRNKEVVFKEPIYVEGSIDSNY 200 210 220 230 240 250


  • identity = the number of perfect matching hit / the number in the field which is considered to be homology. (gap position included)
  • ungapped = the number of perfect maching hit / the numbers in the field which is considered to be homology. (gap position excluded)
  • similar = the hit number of similar amino acid included/ the numbers in the field which is considered to be homology. (gap position included)
 
3 : Change of Web screen lay-out
Specification of retrieval sequence data require to fill the text box of query sequence or file upload function. These text box were moved to the upper part of the screen for users' conveniece.
 
4 : Correspondence of Safari
We have added the correspondence of Safari for FASTA, PSI-BLAST result screen.

5 : Delesion of "C.elegans whole DNA" from retrieval database
At FASTA, BLAST, SSEARCH, we have deleted "C.elegans whole DNA" form the retrieval database of nucleotide sequence database.


 ♦ ClustalW web screen lay-out change and new additional function 
DDBJ provides ClustalW services through WWW and E-mail. In the WWW ClustalW, we modified the data submit screen lay-out, and added some new options as follows.
  • "Sequence input box" is transferred to the top of the page.
  • "TYPE" options became independent from "ALIGN" options group.
  • "AUTOMATIC" was newly added to the the "TYPE" options.
  • When the "AUTOMATIC" is specified in the "TYPE" option, the ClustalW program identifies the sequence type (DNA/Protein) automatically and does the analysis using all default values.
  • "p-distance"was added to the parameters of "DISTANCE" option.
  • "KIMURA" option was integrated into the "DISTANCE" option.

 ♦ Distribution of massive sequence data 
The massive sequence data which were collected by DDBJ and released through the INSD (International Nucleotide Sequence Database) from this June to July are as follows:
Release of 53,359 EST entries for honey bee
DDBJ newly released 53,359 EST entries for honey bee (Apis mellifera), which had been submitted by RIKEN Genomic Sciences Center.
These entries were released as DDBJ daily update on 7/28.
Reference URL: http://genome.gsc.riken.jp/
The accession numbers and the file names for anonymous FTP are as follows;
 
Release of 6970 CON entries for Medaka strain Hd-rR
DDBJ newly released 6970 Medaka strain Hd-rR CON entries, which had been submitted by University of Tokyo. They correspond to the Medaka WGS dataset released on 6/7.
Reference URL: http://medaka.utgenome.org/
The accession numbers and the file names for anonymous FTP are as follows;
  • scaffold/CON DF076466-DF08320 (6741 entries)
    Oryzias_latipes_CON_060608_1.seq.gz
  • ultra/CON DF083207-DF08341 (205 entries)
    Oryzias_latipes_CON_060613_1.seq.gz
  • chromosome/CON DG000001-DG000024 (24 entries)
    Oryzias_latipes_CON_060615_1.seq.gz
These entries were released as DDBJ daily updates on 6/8, 6/13, 6/15, respectively. anonymous FTP
 
Release of new 223 thousand Medaka strain Hd-rR WGS entries
DDBJ newly released 223 thousand Medaka strain Hd-rR WGS entries, which had been submitted by University of Tokyo.
Reference URL: http://medaka.utgenome.org/
The accession numbers are as follows; BAAF03000001-BAAF03223203 (223203 entries)
These entries were released as DDBJ daily updates on 6/7.
All of the data can be retrieved at anonymous FTP site (Oryzias_latipes_WGS_060607_1.seq.gz)
 
Release of 7296 CON entries for Medaka strain Hd-rR
DDBJ newly released 7296 Medaka strain Hd-rR CON entries, which had been submitted by University of Tokyo. They correspond to the Medaka WGS dataset released on 4/21.
Reference URL: http://medaka.utgenome.org/
The accession numbers and the file names for anonymous FTP are as follows;
  • scaffold/CON DF069194-DF076129 (6936 entries)
    Oryzias_latipes_CON_060525_1.seq.gz
  • ultra/CON DF076130-DF076465 (336 entries)
    Oryzias_latipes_CON_060531_1.seq.gz
  • chromosome/CON DG000001-DG000024 (24 entries)
    Oryzias_latipes_CON_060605_1.seq.gz
These entries were released as DDBJ daily updates on 5/25, 5/31, 6/5, respectively.
* Please note some of these CON entries has been updated because of mess-ups of their gap lengths.
anonymousFTP
 
Correction for the "Release of new 31 thousand scaffold/CON entries for Medaka strain Hd-rR (Apr.21)"
The anonymous FTP files corresponding to the announcement of April 21 ("DDBJ newly released 7296 Medaka strain Hd-rR CON entries") has been replaced on June 8 because of mess-ups of their gap lengths. The corrected announcement is as follows:
Release of new 31 thousand scaffold/CON entries for Medaka strain Hd-rR Apr. 21, 2006
DDBJ newly released 31 thousand Medaka strain Hd-rR scaffold/CON entries, which had been submitted by University of Tokyo.
They correspond to the Medaka WGS dataset released on 4/11.
Reference URL: http://medaka.utgenome.org/
The accession numbers are as follows; DF038236-DF069193 (30958 entries)
These entries were released as DDBJ daily updates on 4/14. All of the data can be retrieved at anonymous FTP site (Oryzias_latipes_CON_060524_1.seq.gz).
 
We apologize for your inconvenience.


 ♦ Change of searchable divisions in SRS 
SRS (Sequence Retrieval System) is the keyword retrieval service provided by DDBJ WWW server. After the incorporation of DDBJ release 66 data into SRS database, EST and GSS divisions data will be removed from SRS DDBJRELEASE and DDBJNEW database. Because of the time lag between DDBJ release date (66 was released on June 29) and its loading time to SRS database, this change will be practically refleted to the service around mid to the end of July.
From now, when you want to search EST and GSS division as retrieval targets, we ask you to use ARSA (All-round Retrieval of Sequence and Annotation) for the substitute.
Thank you for your understanding and cooperation.

 ♦ Termination of providing the Blast program on NIG supernig server 
DDBJ will terminate providing the Blast program service which has been provided through NIG supernig server as under test operation, as of July 31, 2006. However, we remain providing BLASTDB which will be placed on $BLASTDB. So, if you install the program by yourself, you can run it by using this DB.
Blast program is available from the following URL: http://ncbi.nih.gov/BLAST/download.shtml

 ♦ Conference on Information Biology 
In the DDBJ HP, we have the page named "Conference on Information Biology". In this page, we introduce the worldwide conferences and the meetings which relate to Genetics, Molecular Biology, Bioinformatics, etc. In this page, the names of conferences are listed by date. It has links so that users can jump to each conference's HP to search for more details. We hope that users refer to this page as the access to information. In addition, our DDBJ staffs involves in some of conferences, so please check these conference for more understanding of DDBJ activities.
Furthermore, if you have any conference information that doesn't listed in our HP, we are welcome to hear the information. Please mail to ddbj@ddbj.nig.ac.jp.

 ♦ STAFF COLUMN 
RNA genes as modulators of gene expression

Roberto Barrero
National Institute of Genetics Gene Function Research Laboratory Assistant Professor

About Science: microRNA genes act as modulators of gene expression
Since the discovery of microRNA (miRNA) genes almost twelve years ago, their crucial role as post-transcriptional regulators in animal and plant species have been demonstrated in the last five years. miRNAs are transcribed from genomes as long primary-precursors (pri-miRNA) , which are processed down into 60-80 nucleotides (nt) precursors (pre-miRNAs) by the Drosha-Pasha processing complex. A single pri-miRNA may encode up to seven pre-miRNAs. The pre-miRNAs are exported to the cytoplasm via the Exportin 5 pathway and are recognize and cleave by Dicer into the mature miRNAs that may range from 21 to 24 nt in lenght. miRNAs guide the RISC (RNA Interference Silencing Complex) to their target genes and mediates either mRNA degradation or translation inhibition.

Currently, there are 1,225 and 392 miRNAs known for animal and plant species, respectively (Rfam Release 6.0). Plant miRNAs usually have perfect complementarities to their target genes binding their coding region and mediating mRNA degradation via the RNA Interference (RNAi) pathway. In contrast, animal miRNAs have imperfect complementarities to their target genes, which prevent a straightforward identification of these targets by in silico approaches. Animal miRNAs will generally bind the 3' untranslated regions (3'UTRs) of their targets that results in inhibition of the protein translation process. The biological functions of miRNAs remain to be uncovered, only for a handful number of miRNAs forward genetics have elucidated their function.

The main interest of our lab is the identification of novel functional RNA genes using comparative genomics. We are focus in the identification of novel microRNA genes in mammalian species. To understand the biology of microRNAs is required to comprehend their genomic context, and evolutionary path. We generated computational tools to identify conserved microRNA genes in human and mouse genomes as well as to investigate the evolution of pri-miRNAs. Linage specific miRNAs may play important roles in defining differences in the gene expression regulation network for each species.

We also developed in silico tools and implemented reporter assay systems to screen and validate highly reliable microRNA-target interactions. The predicted microRNA targets are involved in a wide variety of biological processes implying a crucial role of microRNAs in a number of biological processes such as development, apoptosis, signal transduction and others.

About Life in Mishima: NIG brings many opportunities to do sports at all levels
Two summers had past since I moved to Mishima from Tokyo. At first, there was an obvious "change feeling" from a big metropolis to a more peaceful town. I need no more to take trains in the famous rush hours or run to catch the last train. Some of the first things you hear about Mishima is that the water and air are cleaner, and sure they are! The thing I like most of not having a driving license is that it allowed me to reduce my weight for about 10 kg in my need to ride my bicycle every morning to climb the NIG hill. This was a very effective "diet" strategy given that in one day I may need to repeat the process 2 or 3 times. Now that we can enjoy our NIG cafeteria at noon, the effectiveness of the process has decreased by an approximation of 33%! According to my new gain of weight!! NIG offers everyone the possibility to do various sports such as play soccer, tennis or badminton (as far as I am aware of) and it is very fun to do sports, even the next two days I may not be able to walk straight. The very good thing of doing sports with people at NIG is that everyone can join the group, regardless of their level. Everyone is welcome from first-time beginners to Olympic champions, and the best part of all is that more experienced people will share their knowledge with the rookies. So don't miss the chance to put yourself in shape once in a while!





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