Nakamura Group • Genome Informatics Laboratory
Large-Scale Nucleotide Sequence Analysis and Advancement of Database for Various Organisms
Faculty
Research Summary
Next generation sequencing technologies allow biologists to obtain larger amounts of nucleotide sequence data. It is necessary to provide a high quality genome annotation and versatile database as reference data. It is also important to equip an automated annotation system that makes it possible to get fast and accurate results for reliable sequencing analysis.
Our laboratory is in charge of DNA Data Bank of Japan (DDBJ) and attempts to develop advanced database management systems, and improve the quality of annotations in genome databases. We have been constructing an automatic annotation system for prokaryotes: DDBJ Fast Annotation and Submission Tool (DFAST). We are also providing several high-quality annotated genome information for important plant and animal species such as a liverwort Marchantia polymorpha and a domestic cat Felis catus.
(B) Screenshot of MarpolBase: a liverwort Marchantia polymorpha genome database
Selected Publications
Mochizuki T, Sakamoto M, Tanizawa Y, Nakayama T, Tanifuji G, Kamikawa R, Nakamura Y. A practical assembly guideline for genomes with various levels of heterozygosity. Brief Bioinform. 2023 Sep 22;24(6):bbad337.
Mochizuki T, Sakamoto M, Tanizawa Y, Seike H, Zhu Z, Zhou YJ, Fukumura K, Nagata S, Nakamura Y. Best Practices for Comprehensive Annotation of Neuropeptides of Gryllus bimaculatus. Insects. 2023 Jan 25;14(2):121.
Kawamura S, Romani F, Yagura M, Mochizuki T, Sakamoto M, Yamaoka S, Nishihama R, Nakamura Y, Yamato KT, Bowman JL, Kohchi T, Tanizawa Y. MarpolBase Expression: A Web-Based, Comprehensive Platform for Visualization and Analysis of Transcriptomes in the Liverwort Marchantia polymorpha. Plant Cell Physiol. 2022 Nov 22;63(11):1745-1755.
Tanizawa Y, Fujisawa T, Kodama Y, Kosuge T, Mashima J, Tanjo T, Nakamura Y. DNA Data Bank of Japan (DDBJ) update report 2022. Nucleic Acids Res. 2023 Jan 6;51(D1):D101-D105.
