README file for rgadb of RiceGAAS                                 [2002.11.21]
-----------------------------------------------------------------------------

RiceGAAS (Rice Genome Automated Annotation System) collects the rice genome 
entries in GenBank.

Please see the following URLs about RiceGAAS.

   http://ricegaas.dna.affrc.go.jp
   http://ricegaas.dna.affrc.go.jp/rgadb/
   http://ricegaas.dna.affrc.go.jp/RiceGAAS_system.html

RiceGAAS collects the rice genome entries from the daily-update in GenBank 
database. The collection rules are as follows;

      SOURCE  =  "oryza  sativa"
     and
      9999bp  <  [sequence  size]  <  1Mbp
     not
      DIVISION=  "GSS"  or  "STS"

Each entry from GenBank is categorized into the anchored chromosome, or 
"unknown" if it dose not have any chromosomal information.

Two data set as shown below are made every week.

    GenBank  files
    FASTA  files

-  FTP  files

   ftp://ftp.dna.affrc.go.jp/pub/RiceGAAS/
     +--  20020918   ..   data directory (made at 2002-09-18)
     +--  yyyymmdd   ..   data directory (made at yyyy-mm-dd)
     +--  README     ..   this document
     +--  current    ..   link to the latest data directory

   Data directories in the ftp file above have GenBank files and FASTA files  
   containing the following files below.

-  GenBank files contain the following files.

     RiceGAAS.GenBank.chr01.tar.gz   ..  chromosome   1  genbank  files
     RiceGAAS.GenBank.chr02.tar.gz   ..  chromosome   2  genbank  files
     RiceGAAS.GenBank.chr03.tar.gz   ..  chromosome   3  genbank  files
     RiceGAAS.GenBank.chr04.tar.gz   ..  chromosome   4  genbank  files
     RiceGAAS.GenBank.chr05.tar.gz   ..  chromosome   5  genbank  files
     RiceGAAS.GenBank.chr06.tar.gz   ..  chromosome   6  genbank  files
     RiceGAAS.GenBank.chr07.tar.gz   ..  chromosome   7  genbank  files
     RiceGAAS.GenBank.chr08.tar.gz   ..  chromosome   8  genbank  files
     RiceGAAS.GenBank.chr09.tar.gz   ..  chromosome   9  genbank  files
     RiceGAAS.GenBank.chr10.tar.gz   ..  chromosome  10  genbank  files
     RiceGAAS.GenBank.chr11.tar.gz   ..  chromosome  11  genbank  files
     RiceGAAS.GenBank.chr12.tar.gz   ..  chromosome  12  genbank  files
     RiceGAAS.GenBank.unknown.tar.gz   ..  unknown  genbank  files

   % gunzip RiceGAAS.GenBank.chr01.tar.gz
   % tar tvf RiceGAAS.GenBank.chr01.tar|more
   drwxr-xr-x  100/100        0  2002-04-25  19:51  chr01/
   -rw-r--r--  100/100   145408  2000-03-01  22:40  chr01/10A19I
   -rw-r--r--  100/100   195764  2002-03-26  01:33  chr01/B1085F09
   -rw-r--r--  100/100   193497  2002-03-26  01:34  chr01/OJ1174_D05
   -rw-r--r--  100/100   201668  2002-03-26  01:35  chr01/OSJNBa0025P13
   -rw-r--r--  100/100   209261  2002-03-26  01:25  chr01/OSJNBa0004B13
   -rw-r--r--  100/100   212063  2002-03-26  01:29  chr01/P0666G04
     ::


-  FASTA files contain only the sequence data picked up from GenBank files,
   with comment lines as follows;

   >[Accession No.] ([clone name]) [chromosome No.] [location(cM)] [size(bp)]

   The "location" means the position on the genetic map by RGP shown in the 
   web pages.

     http://rgp.dna.affrc.go.jp/cgi-bin/statusdb/statassign.pl

   FATSA files;
     RiceGAAS.chr01.fasta.gz   ..  chromosome   1  fasta  file
     RiceGAAS.chr02.fasta.gz   ..  chromosome   2  fasta  file
     RiceGAAS.chr03.fasta.gz   ..  chromosome   3  fasta  file
     RiceGAAS.chr04.fasta.gz   ..  chromosome   4  fasta  file
     RiceGAAS.chr05.fasta.gz   ..  chromosome   5  fasta  file
     RiceGAAS.chr06.fasta.gz   ..  chromosome   6  fasta  file
     RiceGAAS.chr07.fasta.gz   ..  chromosome   7  fasta  file
     RiceGAAS.chr08.fasta.gz   ..  chromosome   8  fasta  file
     RiceGAAS.chr09.fasta.gz   ..  chromosome   9  fasta  file
     RiceGAAS.chr10.fasta.gz   ..  chromosome  10  fasta  file
     RiceGAAS.chr11.fasta.gz   ..  chromosome  11  fasta  file
     RiceGAAS.chr12.fasta.gz   ..  chromosome  12  fasta  file
     RiceGAAS.unknown.fasta.gz   ..  unknown   fasta  file

   % gunzip RiceGAAS.chr01.fasta.gz
   % grep "^>" RiceGAAS.chr01.fasta |more
   >10A19I  (10A19I)  chr01  99587bp
   >AP003103  (B1085F09)  chr01  52.7cM  132713bp
   >AP003118  (OJ1174_D05)  chr01  20.2cM  128525bp
   >AP003140  (OSJNBa0025P13)  chr01  58.1cM  133242bp
   >AP003018  (OSJNBa0004B13)  chr01  142268bp
   >AP003047  (P0666G04)  chr01  22.6cM  141983bp
   >AP003074  (OSJNBa0004G10)  chr01  42.4-43.2cM  150379bp
   >AP003104  (OSJNBa0038J17)  chr01  30.5cM  180186bp
     ::


If you have any question, please send e-mail to "support@dna.affrc.go.jp".


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