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. 2022 Jan 7;50(D1):D102-D105.
doi: 10.1093/nar/gkab995.

DNA Data Bank of Japan (DDBJ) update report 2021

Toshihisa Okido  1 , Yuichi Kodama  1 , Jun Mashima  1 , Takehide Kosuge  1 , Takatomo Fujisawa  1 , Osamu Ogasawara  1
Affiliations

DNA Data Bank of Japan (DDBJ) update report 2021

Toshihisa Okido et al. Nucleic Acids Res. .

Abstract

The Bioinformation and DDBJ (DNA Data Bank of Japan) Center (DDBJ Center; https://www.ddbj.nig.ac.jp) operates archival databases that collect nucleotide sequences, study and sample information, and distribute them without access restriction to progress life science research as a member of the International Nucleotide Sequence Database Collaboration (INSDC), in collaboration with the National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute. Besides the INSDC databases, the DDBJ Center also provides the Genomic Expression Archive for functional genomics data and the Japanese Genotype-phenotype Archive for human data requiring controlled access. Additionally, the DDBJ Center started a new public repository, MetaboBank, for experimental raw data and metadata from metabolomics research in October 2020. In response to the COVID-19 pandemic, the DDBJ Center openly shares SARS-CoV-2 genome sequences in collaboration with Shizuoka Prefecture and Keio University. The operation of DDBJ is based on the National Institute of Genetics (NIG) supercomputer, which is open for large-scale sequence data analysis for life science researchers. This paper reports recent updates on the archival databases and the services of DDBJ.

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Figures

Figure 1.
Figure 1.
Overview of genome sequencing, mapping reads, annotation, and registration to INSDC for SARS-CoV-2 samples. In the case of Shizuoka Prefecture, after the National Institute of Genetics (NIG) receives inactive virus samples from Shizuoka Prefecture, NIG conducts several processes: genome sequencing at the Advanced Genomic Center, mapping raw reads to the reference, annotation by DFAST, and variant calls on the NIG supercomputer. After completion of sequencing and computational analysis, NIG reports the summary of the virus genome characteristics to Shizuoka Prefecture. Finally, the virus genome sequences are submitted to both GISAID and DDBJ. In the case of Keio University, sequencing and mapping are performed at Keio University.
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