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          README -- DDBJ anonymous FTP
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This file describes the directory structure and file contents in the DDBJ anonymous FTP site (ftp://ftp.ddbj.nig.ac.jp/ddbj_database/).
For further information on the databases and the file formats, please consult the references listed at the end of this file.

1. DIRECTORY STRUCTURE and FILE CONTENTS

ddbj_database
    |
    |-- README.TXT                            - This file
    |
    |-- bioproject                            - DDBJ BioProject data
    |
    |-- biosample                             - DDBJ BioSample data
    |
    |-- ddbj                                  - The latest release of the DDBJ nucleotide sequence database (in the flat file format)
    |     |
    |     |--  ddbjrel.txt                    - Current release note the DDBJ nucleotide sequence database
    |     |
    |     |--  cdsdb                          - CDS data in the FASTA file format
    |     |
    |     |--  fasta                          - The latest release in the FASTA file format
    |     |
    |     |--  xml
    |            |
    |            |--  insdxml
    |            |      |
    |            |      |--  v1.4             - The latest release in the INSD XML format ver.1.4
    |            |
    |            |--  insdxml_current         - The latest release in the INSD XML format (current version)
    |
    |-- ddbjnew                               - Daily updates after the latest release (in the flat file format)
    |     |
    |     |--  cdsdb                          - CDS data of the daily updates in the FASTA format
    |     |
    |     |--  contig                         - Contig files of the daily updates
    |     |
    |     |--  fasta                          - Daily updates in the FASTA file format
    |     |
    |     |--  qscore                         - Quality score files of the daily updates
    |     |
    |     |--  unified-all                    - Unified dataset of release and daily updates
    |     |      |
    |     |      |--  fasta
    |     |      |
    |     |      |--  blastdb
    |     |
    |     |--  unified-new                    - Unified dataset of daily updates
    |     |      |
    |     |      |--  fasta
    |     |      |
    |     |      |--  blastdb
    |     |
    |     |--  xml
    |            |
    |            |--  insdxml
    |            |      |
    |            |      |--  v1.4             - Daily updates in the INSD XML format ver.1.4
    |            |
    |            |--  insdxml_current         - Daily updates in the INSD XML format (current version)
    |
    |-- dad                                   - The latest release of the DDBJ amino acid sequence database (DAD)
    |     |
    |     |--  dadrel.txt                     - Current release note the DDBJ amino acid sequence database (DAD)
    |
    |-- dadnew                                - Daily updates of the DAD after the latest release (in the flat file format)
    |     |
    |     |--  fasta                          - Daily update of the DAD in the FASTA file format.
    |
    |-- dra                                   - DDBJ/EBI/NCBI Sequence Read Archive data
    |     |
    |     |--  fastq                          - Sequencing data in the FASTQ format and metadata in the XML format
    |     |
    |     |--  sralite                        - Sequencing data in the SRA lite format
    |     |
    |     |--  sra                            - DRA sequencing data in the SRA format
    |     |
    |     |--  meta
    |            |
    |            |--  list                    - List of puclic DRA metadata, data and center name
    |
    |-- dta                                   - Trace data submitted to the DDBJ Trace Archive
    |
    |-- fis                                   - Full insert sequence data of the daily updates
    |
    |-- genomes                               - Completed genome data
    |
    |-- mga                                   - Mass sequence for Genome Annotation data (produced in large quantity in view of genome annotation)
    |
    |-- mass                                  - Repository for large data files supplementarily provided by DDBJ.
    |
    |-- patent                                - Patent amino acid sequence data and list for JPO and KIPO
    |
    |-- release_note_archive
    |     |
    |     |--  ddbj                           - Old release notes of the DDBJ DNA database
    |     |
    |     |--  dad                            - Old release notes of the DDBJ amino acid sequence database
    |     |
    |     |--  16S                            - Old readme files of the 16S rRNA sequence data
    |
    |-- tpa
    |     |
    |     |--  ddbj                           - The latest release of the DDBJ nucleotide TPA sequence database
    |     |      |                              (same tpa file(s) as below ddbj_database-ddbj)
    |     |      |
    |     |      |--  cdsdb                   - CDS data of the daily updates in the FASTA format
    |     |      |
    |     |      |--  fasta                   - The latest release in the FASTA file format
    |     |      |
    |     |      |--  xml                     - The latest release in the INSD XML format ver.1.4
    |     |             |
    |     |             |--  insdxml
    |     |             |      |
    |     |             |      |--  v1.4      - Daily updates in the INSD XML format ver.1.4
    |     |             |
    |     |             |--  insdxml_current  - Daily updates in the INSD XML format (current version)
    |     |
    |     |--  ddbjnew                        - Daily TPA updates after the latest release
    |     |      |
    |     |      |--  cdsdb                   - CDS data in the FASTA file format
    |     |      |
    |     |      |--  fasta                   - Daily updates in the FASTA file format
    |     |      |
    |     |      |--  xml                     - Daily updates in the INSD XML format ver.1.4
    |     |             |
    |     |             |--  insdxml
    |     |             |      |
    |     |             |      |--  v1.4      - Daily updates in the INSD XML format ver.1.4
    |     |             |
    |     |             |--  insdxml_current  - Daily updates in the INSD XML format (current version)
    |     |
    |     |--  wgs                            - WGS TPA reassembly
    |
    |
    |-- tsa                                   - Transcriptome Shotgun Assembly data from GenBank
    |
    |-- wgs                                   - Whole Genome Shotgun sequence data
    |
    |-- 16S                                   - 16S rRNA sequence data extracted from the latest release
    |     |
    |     |--  readme.txt                     - Current readm file of the 16S rRNA sequence data


2. REFERENCES

Release note of the DDBJ nucleotide sequence database
  ftp://ftp.ddbj.nig.ac.jp/ddbj_database/ddbj/ddbjrel.txt

Release note of the DDBJ amino acid sequence database
  ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dad/dadrel.txt

Readme file of the the 16S rRNA sequence data
  ftp://ftp.ddbj.nig.ac.jp/ddbj_database/16S/readme.txt

INSDC Feature Table Document:
  http://www.ddbj.nig.ac.jp/FT/full_index.html

INSD XML format DTD file 
  ftp://ftp.ddbj.nig.ac.jp/ddbj_database/ddbj/xml/insdxml_current/INSD_INSDSeq.dtd


If you have any questions, please use the following addresses.
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Center for Information Biology and DNA Data Bank of Japan
 National Institute of Genetics
 Research Organization of Information and Systems
 
 Mishima 411-8540, Japan 
 Phone:  +81 55 981 6853
 FAX:    +81 55 981 6849
 E-mail: ddbj@ddbj.nig.ac.jp
 WWW:    http://www.ddbj.nig.ac.jp/
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