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. To maximize the utility of the data, it is essential to provide high quality genome annotation and versatile databases as reference resources. 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 while enhancing 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 also provide 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 Cats-I: Cats genome informatics, the genome database for domestic cats
Selected Publications
Elmanzalawi M, Fujisawa T, Mori H, Nakamura Y, Tanizawa Y. DFAST_QC: quality assessment and taxonomic identification tool for prokaryotic Genomes. BMC Bioinformatics. 2025 Jan 7;26(1):3.
Matsumoto Y, Yik-Lok Chung C, Isobe S, Sakamoto M, Lin X, Chan TF, Hirakawa H, Ishihara G, Lam HM, Nakayama S, Sasamoto S, Tanizawa Y, Watanabe A, Watanabe K, Yagura M, Niimura Y, Nakamura Y. Chromosome-scale assembly with improved annotation provides insights into breed-wide genomic structure and diversity in domestic cats. J Adv Res. 2024 Oct 28:S2090-1232(24)00478-8.
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.
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.
