© 2002 Oxford University Press

Nucleic Acids Research, 2002, Vol. 30, No. 1

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DNA Data Bank of Japan (DDBJ) for genome scale
research in life science
Y. Tateno*, T. Imanishi, S. Miyazaki, K. Fukami-Kobayashi, N. Saitou1, H. Sugawara andT. Gojobori
Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Yata, Mishima 411-8540,
Japan and 1Laboratory of Evolutionary Genetics, National Institute of Genetics, Yata, Mishima 411-8540, Japan
Received September 21, 2001; Revised and Accepted October 16, 2001

ABSTRACTThe DNA Data Bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) has made an effort to collect asmuch data as possible mainly from Japanese
researchers. The increase rates of the data wecollected, annotated and released to the public in thepast year are 43% for the number of entries and 52%
for the number of bases. The increase rates areaccelerated even after the human genome wassequenced, because sequencing technology has
been remarkably advanced and simplified, andresearch in life science has been shifted from thegene scale to the genome scale. In addition, we havedeveloped the Genome Information Broker (GIB,
http://gib.genes.nig.ac.jp) that now includes morethan 50 complete microbial genome and Arabidopsis
genome data. We have also developed a database of
the human genome, the Human Genomics Studio(HGS, http://studio.nig.ac.jp). HGS provides one witha set of sequences being as continuous as possible
in any one of the 24 chromosomes. Both GIB andHGS have been updated incorporating newly available
data and retrieval tools.
INTRODUCTION
Since the whole genome of Haemophilus influenzae wassequenced (1), the object of DNA sequencing has been turned
from gene to genome. The success in sequencing of this microbial genome has proven that the shotgun method (2) is efficientenough for sequencing the whole genome not only of
prokaryote but also more complex eukaryote species (3,4). It
can be said that the scope of research in life science has thenbeen shifted from the gene scale to the genome scale. This shift
has long been awaited, because of the assertion that the genes
in an individual organism do not function independently but dointerdependently in complex functional networks. Therefore,
even if one studies the function of a particular gene, one mayhave to extend one’s study to other related genes in the samegenome.

A series of the whole-genome sequencing endeavours haveresulted in sequencing through the whole human genome. The
genome data have then immediately been published both in thejournal (5) and the International Nucleotide Sequence Databases(INSD) that are composed of DDBJ, the EMBL Bank andGenBank. It is noteworthy that the immediate publication ofsuch enormous-scale data was possible perhaps only through awell-established collaboration among the INSD members.
INSD have also provided retrieval and analysis tools by which
one can make the data useful for one’s study. In fact, a large numberof researchers have enjoyed the simultaneous publications of thehuman genome data in print and online.
As a member of INSD, DDBJ has made an effort to collectthe original DNA sequence data, and releasing them to thepublic after annotation. The majority of the data have been
submitted directly from Japanese researchers. We haveexchanged the data thus released with the EMBL Bank andGenBank on a daily basis. This practice allows the three databanks to serve users worldwide with the same quality andquantity of data. We have also developed the Genome
Information Broker (GIB) and the Human Genomics Studio(HGS). Both databases are available now at DDBJ.
DATA COLLECTION AT DDBJTables 1 and 2 show the amounts of data released to the publicfrom the DDBJ submissions at two time points, July 2000 andJuly 2001, respectively. On the whole, the rate of increase in
the past year for the number of entries is 43.0% and for thenumber of bases is 51.6% indicating that the number of basesin an entry has been increased. This implies that the contribution
from various genome groups in Japan has been increased in thepast year. Usually, a genome team tends to submit an entry
including a larger number of bases than other entries. Thistendency is clarified more if we focus on the items (taxonomicdivisions) in the tables.
In the past year the Japanese human genome teams made asignificant contribution to the international human genome
sequencing consortium. We at DDBJ established a goodcollaboration with them to make it possible to collect andimmediately release their large-scale data to the public. Thedata include a part of the entire HLA region in chromosome 6*To whom correspondence should be addressed. Tel: +81 559 81 6857; Fax: +81 559 81 6858; Email: ytateno@genes.nig.ac.jp
Present address:
T. Imanishi, Japan Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Aomi, Koto-ku, Tokyo 135-0064, Japan

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Table 1. The number of entries made public from the DDBJ submissions

aEach division is as follows. (taxonomy) HUM: human, PRI: primate, ROD: rodent, MAM: mammal, VRT: vertebrate,
INV: invertebrate, PLN: plant and fungi, BCT: bacteria, VRL: virus, PHG: bacteriophage, SYN: synthesized sequence;(sequence quality) EST: expressed sequence tag, GSS: genome survey sequence, HTG: high-throughput genomic
sequence; (other) STS: sequence tagged site, UNA: unannotated sequence; (patent) PAT: patent data.
bThe number in parentheses is the percentage of genome data to the total of each division.
c%∆ is the rate of increase in the year.

Table 2. The number of bases (bp) made public from the DDBJ submissions(6), parts of chromosomes 22 (7) and 21 (8). In Tables 1 and 2,
the HUM division shows the number of entries and the numberof bases, respectively, of human sequence data. The number inthe parentheses is the ratio of the data submitted from theJapanese human genome teams in percentage. The HUM
division in Table 2 indicates that >70% of the bases have been
submitted from the genome teams. In contrast, thecorresponding division in Table 1 shows that <10% of theNucleic Acids Research, 2002, Vol. 30, No. 129Figure 1. The homepage of the Human Genomics Studio.

entries have been submitted from the genome teams. Thesetwo contrasting figures confirm the above-mentioned
tendency. The rates of increase for this division both in thenumber of entries and of bases exceed the average rates over
the all divisions. It is also noted that the majority of the HTG
division is human genome sequence data in the pre-assembled
status. As is clear in Table 1, all data in this division have been
contributed from the genome teams.
Similar observations to the HUM division can be made for
the ROD, PLN and BCT divisions in Tables 1 and 2. Amongthem, it is particularly noteworthy that the rice gemone team of
the National Institute of Agrobiological Resources and theArabidopsis team of the Kazusa DNA Institute (9) have madesignificant contributions to the PLN division. Also noteworthy
is that several genomes of bacterial species, Buchunera sp.
(10), Bacillus halodurans (11), Chlamydia pneumoniae (12),Mesorhizobium loti (13), Staphylococcus aureus (14) andothers, have been sequenced and submitted in the past year.
Consequently, the BCT division has been on a remarkableincrease both in the number of bases and the ratio of genome
sequence data as shown in Table 2.
Most of the Japanese genome teams now use our mass
submission tool, MST (15), for submitting their data to DDBJ.
In this case we can easily sort out the genome data from theothers in a division by searching for particular accession
numbers given to a genome team. There are, however, cases inwhich sorting out cannot be carried out easily. The Silver

Genome Project of our institute for sequencing ape genome(http://sayer.lab.nig.ac.jp/~silver/) is one of them. That is whythe PRI division in Tables 1 and 2 shows no ratio of genome
data in spite of the fact that the project has made an outstanding
contribution to the PRI division.
SPECIALIZED DATABASES DEVELOPED AT DDBJ
Our prime mission is of course to collect the original DNA
data, and release them to the public after annotation. In
addition to the mission we have extended our annotation
capacity to collaborating with the Riken mouse project (16)and to developing and updating several specialised databaseson the basis of our DNA database. One of these databases is theGenome Information Broker of the complete genome sequence
data (GIB, http://gib.genes.nig.ac.jp) (17). Since its original
version, GIB has been updated incorporating newly publishedcomplete genome sequence data and new retrieval tools. GIB
at present includes more than 50 complete bacterial genome
sequences and the complete yeast and Arabidopsis genome
sequences. One can carry out homology and keyword searches
for one particular species or all across the species in GIB.
Therefore, for instance, GIB may enable one to simultaneously
investigate the evolution of a set of functionally related genes
both in prokaryote and eukaryote species. It may also help one
with studying the relationships between the location of related
genes and their functional aspects.

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Another specialised database is the Human Genomics Studio(HGS, http://studio.nig.ac.jp). The home page of HGS isshown in Figure 1. We started developing HGS just before thewhole human genome sequence data were published. There aremainly four aims of developing HGS: (i) to reconstruct thewhole human chromosomes collecting and assembling all theavailable sequence data, (ii) to map all the available genes on
the chromosomes, (iii) to compile a human gene catalog
containing information about the function, relationships
among genes, size, polymorphism and so forth, and (iv) toprovide anyone with those data being as complete and updated
as possible. We have provided part of the first aim through theabove web site and are working on the rest.
CONCLUDING REMARKS
Genome sequencing has raised one problem despite having
made a profound contribution to life science. It is noted firstthat a submitted genome sequence often includes possible
genes, which were inferred by computer tools. These genes
may be called in silico genes. The problem is that an in silico
gene is determined by the algorithm and arbitrarily given
parameters of the computer tool not by experiment.
Moreover, a different tool produces different genes for thesame sequence. This creates the undesirable chain reaction that
one user writes a paper mistakenly regarding in silico genes asreal ones and then another follows citing this spurious paper
without carefully examining it. There is, however, an international
movement which would issue the recommendation that INSD
should encourage a data submitter to distinguish in silico genes
from experimentally obtained ones. If this recommendation is
implemented, DDBJ will act on it.
ACKNOWLEDGEMENTS
We thank the rest of the DDBJ members for making it possible
to run well this international DNA data bank. We are also
grateful to the Ministry of Education, Science, Culture, Sports
and Technology for their enduring financial support.
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