DNA data bank of Japan (DDBJ) progress report

Abstract

The DNA Data Bank of Japan Center (DDBJ Center; http://www.ddbj.nig.ac.jp) maintains and provides public archival, retrieval and analytical services for biological information. The contents of the DDBJ databases are shared with the US National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI) within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). Since 2013, the DDBJ Center has been operating the Japanese Genotype-phenotype Archive (JGA) in collaboration with the National Bioscience Database Center (NBDC) in Japan. In addition, the DDBJ Center develops semantic web technologies for data integration and sharing in collaboration with the Database Center for Life Science (DBCLS) in Japan. This paper briefly reports on the activities of the DDBJ Center over the past year including submissions to databases and improvements in our services for data retrieval, analysis, and integration.

How Many Plant Species are There, Where are They, and at What Rate are They Going Extinct?

“…While our reference library represents a significant advance in plant DNA metabarcoding, our rbcL reference library and the ITS2 reference library of Sickel et al (2015) fall far short of being comprehensive. There are an estimated 450,000 flowering plant species on earth (Pimm (Benson et al, 2015), the DNA Data Bank of Japan (DDBJ; Mashima et al, 2015), and the European Molecular Biology Laboratory (EMBL) Nucleotide Sequence Database (Squizzato et al, 2015), do not require researchers submitting sequences to provide links to voucher specimens or raw sequence data, and may include sequences with incorrect species identification or low-quality sequence data. Other databases, such as the Barcode of Life Database (BOLD; Ratnasingham and Hebert, 2007), have stringent quality control but fewer plant rbcL sequences than the NCBI database, and no plant ITS2 sequences.…”

Pollen DNA barcoding: current applications and future prospects

“…A current compromise is to rely on public sequence databases that may contain high coverage of species for a given habitat. For plants, the largest sources for reference sequencing data are the redundant repositories NCBI (Benson et al 2015), EMBL (Squizzato et al 2015), and DDBJ (Mashima et al 2015). There are over 32 million vascular plant nucleotide sequences deposited, although only a fraction of these represent DNA barcoding markers (see Table 1 for the number of sequences associated with each of the standard DNA barcoding markers).…”

Pseudomonas aeruginosa Type III Secretory Toxin ExoU and Its Predicted Homologs

“…Aeromonas , a Gram-negative, facultative anaerobic and rod-shaped bacterium, is ubiquitous in fresh and brackish water [48]. Most Aeromonas species are known to be associated with human diseases.…”

“…The sequence alignment was made by ClustalW with the BLOSUM protein weight matrix (DNA Data Bank of Japan) [48]. …”

“…( a ) The amino-terminal alignment for predicted ExoU homologs; ( b ) the carboxyl-terminal alignment for predicted ExoU homologs. The sequence alignment was made by ClustalW with the BLOSUM protein weight matrix (DNA Data Bank of Japan) [48]. …”