DDBJ progress report.

DDBJ progress report
Eli Kaminuma, Takehide Kosuge, Yuichi Kodama, Hideo Aono, Jun Mashima,
Takashi Gojobori, Hideaki Sugawara, Osamu Ogasawara, Toshihisa Takagi,
Kousaku Okubo and Yasukazu Nakamura*
Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics,
Research Organization for Information and Systems, Yata, Mishima, 411-8510, Japan
Received September 27, 2010; Revised October 7, 2010; Accepted October 11, 2010
ABSTRACT
The DNA Data Bank of Japan (DDBJ, http://www
.ddbj.nig.ac.jp) provides a nucleotide sequence
archive database and accompanying database
tools for sequence submission, entry retrieval and
annotation analysis. The DDBJ collected and
released 3 637 446 entries/2 272 231 889 bases
between July 2009 and June 2010. A highlight of
the released data was archive datasets from
next-generation sequencing reads of Japanese
rice cultivar, Koshihikari submitted by the National
Institute of Agrobiological Sciences. In this period,
we started a new archive for quantitative genomics
data, the DDBJ Omics aRchive (DOR). The DOR
stores quantitative data both from the microarray
and high-throughput new sequencing platforms.
Moreover, we improved the content of the DDBJ
patent sequence, released a new submission tool
of the DDBJ Sequence Read Archive (DRA) which
archives massive raw sequencing reads, and
enhanced a cloud computing-based analytical
system from sequencing reads, the DDBJ Read
Annotation Pipeline. In this article, we describe
these new functions of the DDBJ databases and
support tools.
INTRODUCTION
The DNA Data Bank of Japan (DDBJ, http://www.ddbj
.nig.ac.jp) is one of the three databanks that comprise the
DDBJ/EMBL-Bank/GenBank International Nucleotide
Sequence Database (INSD), which was established
through close collaboration with the European
Bioinformatics Institute (EBI) in Europe and the
National Center for Biotechnology Information (NCBI)
in the USA. The DDBJ is administered by the Center
for Information Biology and DDBJ (CIB-DDBJ) of the
National Institute of Genetics (http://www.nig.ac.jp/
index-e.html) with funding endorsement from the
Japanese Ministry of Education, Culture, Sports, Science
and Technology (MEXT). All researchers can submit
their data to one of the three summit databanks to
register it with the INSD. The enrolled data are exchanged
every day, so the three collaborating databanks share vir-
tually the same data at any given time. In this report, we
introduce advances in the DDBJ databases and related
services based on the updates from last year.
Specifically, we describe new entries in the DDBJ data-
bases, a new archive database for quantitative biological
data and improvements in the database services of data
registration, analysis and retrieval. All resources are
available from http://www.ddbj.nig.ac.jp/index-e.html,
and archive data can be downloaded at ftp://ftp.ddbj
.nig.ac.jp/.
RECENT DATA GROWTH IN DDBJ DATABASES
Development of DDBJ primary databases
Here, we introduce the development of the DDBJ
database as a member of the INSD during the course of
2010, which is appended to last year’s report (1). Between
July 2009 and June 2010, 14 296 738 entries/
10 572 329 252 bp were released from the INSD as core
traditional nucleotide flat files, except for whole-genome
shotgun (WGS), mass sequence for genome annotation
(MGA) and third party annotation (TPA) files (2). The
DDBJ collected and released original data consisting of
3 637 446 entries/2 272 231 889 bp during this period. The
DDBJ contributed 25.4% of the entries and 21.5% of the
base pairs added to the INSD during this period. Most of
the nucleotide data were submitted from Japanese re-
searchers; the rest came from China, Korea, Taiwan and
other countries. The DDBJ has also continually
distributed patent data transferred from the Japan
Patent Office (JPO, http://www.jpo.go.jp/index.htm) and
the Korean Intellectual Property Office (KIPO, http://
www.kipo.go.kr/en/). In addition to the core nucleotide
data, the DDBJ has released a total of 2 049 801 WGS
entries, 35 270 259 MGA entries and 628 TPA entries as
of 21 September 2010.
*To whom correspondence should be addressed. Tel: +81 55 981 6859; Fax: +81 55 981 6889; Email: yanakamu@genes.nig.ac.jp
D22–D27 Nucleic Acids Research, 2011, Vol. 39, Database issue Published online 9 November 2010
doi:10.1093/nar/gkq1041
� The Author(s) 2010. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/
by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

In addition to traditional nucleotide data, the DDBJ
has released raw sequencing data output from the DDBJ
Trace Archive (DTA, http://trace.ddbj.nig.ac.jp/dta/dta_
index_e.shtml) and the DDBJ Sequence Read Archive
(DRA, http://trace.ddbj.nig.ac.jp) (3). The DTA
contains raw sequencing data obtained from gel/capillary
platforms such as Applied Biosystems ABI 3730. The
DRA collects raw data from next-generation sequencing
platforms (NGSes). As of 21 September 2010, the DDBJ
has released 2 DTA submissions and 32 DRA
submissions.
Noteworthy large-scale data released from the DDBJ
are listed in Table 1. The genome data for Japanese rice,
Oryza sativa Japonica Group cultivar Nipponbare, under-
went an important update (4). With this update, the rice
chromosome version was changed from build 3 to build 4,
and approximately 28 000 coding sequence features were
annotated to the genome as a result of the Second Rice
Annotation Project Meeting (RAP2), managed by the
International Rice Genome Sequencing Project (5)
(http://rapdb.dna.affrc.go.jp/). The DDBJ released
WGS, scaffold and DRA datasets obtained from the
Japanese rice cultivar Koshihikari, which were submitted
by the National Institute of Agrobiological Sciences (6).
Koshihikari is the most popular rice in Japan; it has
occupied the most cultivated rice acreage for the last 30
years. Since the genome sequence of the japonica rice
cultivar Nipponbare has been reported, the Koshihikari
data will be useful for comparative genome analysis
among rice cultivars.
Moreover, the DDBJ has released the expressed
sequence tags (ESTs) of eggplant (Solanum melongena)
and turkey berry (Solanum torvum) submitted by the
National Institute of Vegetable and Tea Science, Japan;
the tomato (Solanum lycopersicum) WGS submitted by the
Kazusa DNA Research Institute; the Vigna radiata WGS
submitted by the National Center for Genetic Engineering
and Biotechnology, Thailand; the Drosophila melanogaster
MGA submitted by the National Institute of Advanced
Industrial Science and Technology, Japan; the false killer
whale (Pseudorca crassidens) genome survey sequence
(GSS) submitted by the Korea Research Institute of
Bioscience and Biotechnology; the Sus scrofa EST
submitted by the National Institute of Agrobiological
Sciences, Japan; the Mus musculus MGA submitted by
Kinki University, Japan; the tomato (Solanum
lycopersicum) GSS submitted by the University of
Tsukuba, Japan; the Mus musculus domesticus GSS
submitted by the RIKEN BioResource Center; the
purple witchweed (Striga hermonthica) EST submitted by
RIKEN; the Mus musculus MGA submitted by the
National Institute of Neuroscience, Japan and both GSS
and EST data for fission yeast (Schizosaccharomyces
pombe) from Osaka City University, Japan.
Development of DDBJ secondary databases
A secondary database is constructed by re-analyzing or
modifying the primary data consisting of nucleotide
sequence flat files released from the INSD. The DDBJ
provides users with various types of secondary databases.
DDBJ Amino Acid Database (DAD) records amino acid
sequences extracted from values of /translation qualifiers
in the nucleotide flat files. The DAD consists of 17 348 613
entries (4 825 871 820 amino acids) as of June 2010. Gene
Trek in Prokaryote Space (GTPS, http://gtps.ddbj.nig.ac
.jp/) (7) is a prokaryotic genome database that has been
re-annotated by a sophisticated common protocol. GTPS
assigns reliability grades to entire re-annotated
protein-coding genes according to the result of blast and
motif scans. GTPS can predict genes that are not
annotated originally. As of 21 September 2010, GTPS
Table 1. List of large-scale data released from the DDBJ from July 2009 to June 2010
Type Organism Accession number (number of entries)
Genome (update) Rice (Oryza sativa Japonica Group, cultivar Nipponbare) AP008207–AP008218 (12)
EST Eggplant (Solanum melongena) FS000001–FS098086 (98 086)
EST Turkey berry (Solanum torvum) FS098087–FS126465 (28 379)
WGS Tomato (Solanum lycopersicum) BABP01000001–BABP01100783 (100 783)
WGS Vigna radiata BABL01000001–BABL01046645 (46 645)
MGA Drosophila melanogaster AMAAA0000001–AMAAA0023916 (23 916);
AMAAB0000001–AMAAB0024086 (24 086)
GSS False killer whale (Pseudorca crassidens) DE647769–DE737775 (90 007)
EST Sus scrofa FS639971–FS722296 (82 326)
MGA Mus musculus ANAAA0000001–ANAAA0033164 (33 164);
ANAAB0000001–ANAAB0051442 (51 442)
GSS Tomato (Solanum lycopersicum) FT227487–FT321168 (93 682)
GSS Mus musculus domesticus DH839446–DH961576 (122 131)
EST Purple witchweed (Striga hermonthica) FS438984–FS506797 (67 814)
WGS scaffold DRA Rice (Oryza sativa Japonica Group, cultivar Koshihikari) BABO01000001–BABO01654543 (654 543);
DG000025–DG000036(12); DRA000010
MGA Mus musculus ALAAA0000001–ALAAA0130942 (130 942);
ALAAB0000001–ALAAB0116883 (116 883);
ALAAC0000001–ALAAC0092019 (92 019);
ALAAD0000001–ALAAD0057749 (57 749)
GSS EST Fission yeast (Schizosaccharomyces pombe) FT321169–FT434719 (113 551);
FY072959–FY174037 (101 079)
Nucleic Acids Research, 2011, Vol. 39, Database issue D23

contains 862 bacterial (Archaea and Eubacteria) genomes.
The GTPS database is updated once a year. In addition to
this periodic update, the entire GTPS dataset will soon be
updated, and about 1000 bacterial genomes will be
re-annotated. The Genome Information Broker (GIB,
http://gib.genes.nig.ac.jp/) (8) is a comprehensive data re-
pository of complete microbial genomes in the public
domain. It collects complete bacterial genome sequences
and annotations soon after the data are available in the
INSD. As of 21 September 2010, 1238 genomes of bacter-
ial strains are stored in the GIB. The Genome Information
Broker for Viruses (GIB-V, http://gib-v.genes.nig.ac.jp/)
(9) is a repository of complete virus genomes or segment
data automatically collected from INSD release data.
As of 21 September 2010, 69 294 viral genomes and
segments can be obtained from the GIB-V. Genomes
TO Protein structures and function (GTOP) (10) is a
database consisting of data analyses of proteins identified
by genome projects. The GTOP database mainly uses
sequence homology analysis and information on 3D
structures.
NOVEL DATABASE SERVICES
DDBJ Omics Archive: new archive for quantitative
genomics data
Next-generation sequencing platforms are gradually
replacing the DNA microarray for measuring molecular
abundances at the genomic scale. To accommodate quan-
titative genomics data from traditional and new platforms,
the DDBJ has decided to launch a new archival database,
the DDBJ Omics aRchive (DOR). The DOR has agreed to
collaborate with ArrayExpress at the EBI to exchange
data. The DOR archives data in compliance with two
international guidelines, Minimum Information about a
High-Throughput Sequencing Experiment (MINSEQE)
and Minimum Information about a Microarray
Experiment (MIAME), as ArrayExpress does (11). As
NGSes are used to quantify DNA/RNA molecules, re-
searchers submit their raw data to the DRA and their
processed data to the DOR. The DOR will establish a
submission brokering system in which researchers
deposit necessary data sets to the DOR, and the raw
data are automatically registered to the DRA.
The DDBJ has supported a microarray database, the
Center for Information Biology Gene Expression
database (CIBEX, http://cibex.nig.ac.jp) (12) by providing
maintenance service. The DOR integrates CIBEX data
and exports the data to ArrayExpress (13).
IMPROVEMENTS IN DATABASE SERVICES
DDBJ patent sequence database: amino acid entries
We also enhanced the patent sequence databases and
added new search and download services. The DDBJ
has maintained two patent sequence databases, JPO and
KIPO, which consist of patent sequences originally
included in patent publications. These databases supply
information in DDBJ patent flatfile format and include
patent information since 1997. The first enhancement of
the DDBJ patent sequence databases was to add
taxonomic organism information to all DDBJ flatfiles.
This was done as follows. First, the NCBI taxonomy ID
was added as the taxon in the /db_xref qualifier on the
basis of the original organism names in data submitted to
JPO and KIPO. Next, individual organism qualifiers/
organism, were added using taxon information. Then,
the common name on the SOURCE line was similarly
appended. Finally, the lineage on the ORGANISM line
was constructed. As a result, we have released the revised
nucleic acid and amino acid entries for JPO and KIPO
beginning in May 2010. The organism information will
be updated once per year. The second enhancement of
these databases is to append amino acid patent sequences
for anonymous FTP download and BLAST search.
Beginning February 2010, DDBJ’s anonymous FTP site,
ftp://ftp.ddbj.nig.ac.jp/ddbj_database/patent/, has
provided the cumulated amino acid sequences for JPO
and KIPO with gzip compression. Moreover, beginning
August 2010, DDBJ’s BLAST search service has con-
tained databases of amino acid sequences from the JPO,
KIPO, EPO (European Patent Office) and USPTO
(United States Patent and Trademark Office).
MetaDefine: new web-based submission tool of DRA
The DRA (http://trace.ddbj.nig.ac.jp) is an archival
database for data from the primary analysis phase of
next-generation sequencing. The DRA has constructed a
world-wide Sequence Read Archive (SRA) by mirroring
data with partner databases at the NCBI and EBI (3). To
support efficient data submission to the DRA, we imple-
mented a novel web-based metadata creation tool,
MetaDefine, for the submission system (Figure 1).
Instead of generating complex XML files, submitters can
create metadata by simply entering the necessary informa-
tion in the MetaDefine interface. Submitters can also
create metadata by editing an existing submission or a
template (e.g. Transcriptome) offered by the tool.
MetaDefine validates the metadata’s format and content
and displays detailed error messages to help users prepare
valid metadata.
DRA provides all public SRA data by FTP in FASTQ
files (ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/). A data
retrieval system will soon be available. The DRA con-
tinues to automate the submission process and support
data from new sequencers as a platform database.
DDBJ Read Annotation Pipeline: functional reinforcement
The DDBJ Read Annotation Pipeline (DDBJ Pipeline,
http://p.ddbj.nig.ac.jp) annotates NGS raw sequencing
reads with high-throughput (Figure 2). The DDBJ
Pipeline is a cloud computing-based pipeline analysis
system, so users can access National Institute of
Genetics (NIG) supercomputers through a web applica-
tion with a graphical user interface. The DDBJ Pipeline
consists of two processes: a basic analytical process for
reference sequence mapping and de novo assembly, and
an analytical process for structural and functional
D24 Nucleic Acids Research, 2011, Vol. 39, Database issue

annotations. In the basic process, popular mapping and
assembly tools are available, and reference sequences can
be retrieved by INSDC accession from the DDBJ
database using SOAP access (14). Analytical statistics on
the mapping error rate by read positions, ratio of mapped
reads, coverage, sequence depth and maximum contig
length can be generated. The analytical process is current-
ly implemented, and several tools for detecting single nu-
cleotide polymorphisms (SNPs) and deletion/insertion
polymorphisms (DIPs) are available. The DDBJ Pipeline
was enhanced by release of the following functions.
(i) Color-space support.
(ii) Ability to upload local query files (FASTA format)
without DRA registration.
(iii) Ability to upload original reference sequences.
(iv) Email notification of job completion/errors.
(v) Improved computational performance.
(vi) Security support.
The color-space analytical tools of LifeTech SOLiD are
supported. In addition to the ability to start from
FASTQ-formatted files, which are generated from DRA
raw files, the pipeline enables the use of users’ original
FASTA-formatted files to start without registration by
uploading from a local computer. Data registration to
the DRA is not required for trial data, and thus the
DRA issues a temporary accession number. Moreover,
original reference sequences can be uploaded. When jobs
are finished or aborted, users receive email notification.
The infrastructure has been improved from 128 GB of
memory to 256 GB for de novo assembly. To enhance
security, Hypertext Transfer Protocol Secure (HTTPS)
has been made available.
In de novo assembly, a metadata file of the DDBJ WGS
category is automatically generated for convenience in
subsequent submissions to the DDBJ database. In the
future, the DDBJ Pipeline will also support RNA-seq
workflow and submission to the DOR database.
Figure 1. Web-based metadata creation tool MetaDefine implemented in DRA submission system.
Nucleic Acids Research, 2011, Vol. 39, Database issue D25

ACKNOWLEDGEMENTS
We gratefully acknowledge the support of all members of
the DDBJ for data collection, annotation and release and
for software development. In particular, we thank Takako
Mochizuki, Dr Hideki Nagasaki, Dr Toshihisa Okido and
Dr Satoshi Saruhashi for consultations on the DRA and
the pipeline and Professor Yoshio Tateno for support in
the form of database maintenance and INSD
collaboration.
FUNDING
Ministry of Education, Culture, Sports, Science and
Technology of Japan with a management expense grant
for national university cooperation (to DDBJ); Integrated
Database Project (http://lifesciencedb.jp/en) of the
Database Center for Life Science in Japan (to DDBJ
Trace Archive, DDBJ Sequence Read Archive and
DDBJ Pipeline, partially); Institute for Bioinformatics
Research and Development, Japan Science and
Technology Agency (to DDBJ Trace Archive, DDBJ
Sequence Read Archive and DDBJ Pipeline, partially).
Funding for open access charge: The DDBJ management
expenses grant.
Conflict of interest statement. None declared.
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Figure 2. Cloud computing-based NGS analytical tool DDBJ Pipeline. Present running status of all jobs can be viewed in the Status panel.
D26 Nucleic Acids Research, 2011, Vol. 39, Database issue