Genome Informatics Laboratory • Nakamura Group

Promotion of DDBJ as an infrastructure database for lifescience

Faculty

 

Research Summary

Ultra high-throughput sequencing technologies allow biologists to obtain larger amounts of nucleotide sequence data. Reliable database operation and high-quality annotation supply are essential. As the core part of DNA Data Bank of Japan (DDBJ), Nakamura laboratory attempts 1) to develop advanced database management systems, and 2) to improve quality of annotations in DDBJ databases. We have been constructing an automatic analytical system “DDBJ Read Annotation Pipeline” in NIG supercomputers, and “TogoAnnotation” system as the integrated support tool for manual curations. Structural and functional annotations by automatic and manual processing are evaluated by using proposed statistical methods.

A screenshot of reference mapping tools on a NGS automatic analytical system

Publications

Mashima, J., Kodama, Y., Kosuge, T., Fujisawa, T., Katayama, T., Nagasaki, H., Okuda, Y., Kaminuma, E., Ogasawara, O., Okubo, K., Nakamura, Y., and Takagi, T. (2016). DNA data bank of Japan (DDBJ) progress report. Nucleic Acids Res 44, D51-57.

Ohyanagi, H., Ebata, T., Huang, X., Gong, H., Fujita, M., Mochizuki, T., Toyoda, A., Fujiyama, A., Kaminuma, E., Nakamura, Y., Feng, Q., Wang, Z.X., Han, B., and Kurata, N. (2016). OryzaGenome: Genome Diversity Database of Wild Oryza Species. Plant Cell Physiol 57, e1.

Tanizawa, Y., Tohno, M., Kaminuma, E., Nakamura, Y., and Arita, M. (2015). Complete genome sequence and analysis of Lactobacillus hokkaidonensis LOOC260 (T), a psychrotrophic lactic acid bacterium isolated from silage. BMC Genomics 16, 240.