National Institute of Genetics

What National Institute of Genetics does

National Institute of Genetics (NIG; 国立遺伝学研究所) is a Japanese national inter-university research institute operating as part of the Research Organization of Information and Systems (ROIS; 大学共同利用機関法人 情報・システム研究機構). Established in 1949 and headquartered in Mishima, Shizuoka Prefecture, NIG operates Japan's principal public infrastructure for genetic and genomic research across five academic departments covering genome evolution, genetic mechanisms, genetics, chromosome science, and frontier fields. The institute employs 101-250 staff and operates the DNA Data Bank of Japan (DDBJ), one of only three internationally recognized nucleotide sequence databases worldwide, alongside NCBI/GenBank and the European Nucleotide Archive.

NIG's core technology stack centers on bioinformatics infrastructure and experimental genomics. Key software products include DFAST (DDBJ Fast Annotation and Submission Tool) and its API/standalone variants for prokaryotic genome annotation, DFAST_QC for quality assessment, MicrobeDB.jp for microbial and metagenomic data, CRISPRdirect for guide RNA design, PZLAST for metagenomic similarity search, VITCOMIC2 for taxonomic assignment, and the Metagenomic Thermometer for paleoenvironmental inference. The institute maintains supercomputer systems, the Integrated Research Core (NIGiRC), and the National BioResource Project (NBRP) distribution channels for mouse, plant, and microbial strains. Recent product launches in 2026 include PZLAST-MAG (May), Microbiome Datahub (March), and AutoFixMark (February).

NIG is fully government-funded under Japan's national research institute framework and does not operate as a commercial enterprise. Revenue is derived from MEXT-aligned ministry budgets via ROIS, supplemented by competitive scientific grants. Services and database access are provided at no cost or via institutional arrangements. The institute reaches academic researchers worldwide through web platforms, the NIG-JOINT joint research program, NIG Colloquia, biological symposia, annual Open House events, and the SOKENDAI graduate program. Industry engagement is facilitated through the Research & Innovation Bridge Center, the Industry-Academia Collaboration Office, and recent partnerships such as the Kyowa Kirin collaboration on Tol2 transposon-based recombinant protein production.

Name

National Institute of Genetics

Legal name

National Institute of Genetics

Website

https://nig.ac.jp

Company type

Private

Founded year

1985

Operating status

Operating

Headcount range

101–250 employees

Short description

The National Institute of Genetics (NIG) is Japan's national inter-university research institute operating the DNA Data Bank of Japan (DDBJ), one of three global nucleotide databases, and providing bioinformatics tools (DFAST, MicrobeDB.jp, CRISPRdirect), bioresources, and graduate education through SOKENDAI to academic researchers worldwide.

Ownership category

akta.pro rank

Product category

Genetics & Genomics Research Services

NAICS

Research and Development in Biotechnology (except Nanobiotechnology) (541714)

SIC

Services-Commercial Physical & Biological Research (8731)

akta.pro primary industry

Genomics & Next-Generation Sequencing (NGS) Services (HLAGANAA)

akta.pro secondary industries

Molecular & Genetic Testing (PCR/NGS/qPCR) (HLAGADAF), Laboratory-Based Surveillance & Genomic Epidemiology (WGS/NGS) (HLAJABAC), Molecular Biology & Genomics Instruments (PCR/qPCR, Sequencing, Microarrays) (HLAGAIAF)

Keywords

• Genetics research
• Bioinformatics databases
• Genome analysis
• Biological resources
• Life sciences research

Headquarters

HQ city

Mishima

HQ country

Japan

HQ region

Asia

Offices1 record

Markets served

GTM type

B2B

Offering type

Services

Cost components

Personnel, Technology or R&D, Infrastructure, Operations

Revenue model

1. Government Funding: As an inter-university research institute under the Research Organization of Information and Systems (ROIS), NIG is primarily funded through the Japanese government's ministry budgets for national research institutions. Core operational funding comes from the National Institute for Academic Research and Education.

Go-to-market motion1 record

Distribution channels3 records

Marketing channels5 records

Core offering

National Institute of Genetics (NIG) is a Japanese national research institute that conducts genetics and genomics research, develops and operates bioinformatics databases and genome analysis tools (including DDBJ, DFAST, MicrobeDB.jp, CRISPRdirect), preserves and distributes biological resources (mouse, plant, and microbial strains) through the National BioResource Project, and provides graduate education through SOKENDAI. It serves as a core facility for genome data management and collaborative research in Japan.

Product overview

The National Institute of Genetics operates as a research-focused institution providing bioinformatics databases, genome analysis tools, and biological resources rather than a traditional product company. Its core offerings center on DFAST (DDBJ Fast Annotation and Submission Tool) - a prokaryotic genome annotation pipeline available as web service, API, and standalone software - and related tools including DFAST_QC for quality assessment. The institution maintains major biological databases including MicrobeDB.jp for microbial genomics, Cats-I for cat genome informatics, and the NIG Mouse Genome Database (NIG_MoG2). Additional research tools include CRISPRdirect for CRISPR guide RNA design, PZLAST for metagenomic sequence search, VITCOMIC2 for taxonomic assignment, Metagenomic Thermometer for environmental prediction, and the refex reference expression dataset. Research infrastructure includes the NIG Supercomputer System, Integrated Research Core (NIGiRC), and the NIG-JOINT collaborative research program. Educational offerings include the NIG Method scientific presentation training curriculum.

Differentiator

Problem solved

Functional benefit

Brands

• DFAST: A bioinformatics web service developed by Nakamura Group for automated prokaryotic genome annotation, integrated with DDBJ submission support.
• MicrobeDB.jp
• Cats-I
• PZLAST-MAG
• XMRs (Thing Metabolome Repository family)
• NIG Method

Products and services

• DFAST (DDBJ Fast Annotation and Submission Tool) A web-based prokaryotic genome annotation pipeline integrated with quality and taxonomy assessment methods, enabling preparation of DDBJ Mass Submission System files for the complete genome annotation workflow.
• DFAST Web API Programmatic interface for command-based genome annotation job management including job submission, status checking, data downloading, and job deletion via REST API endpoints.
• DFAST-core Standalone version of the DFAST annotation pipeline bundling external binaries for installation via Bioconda, supporting flexible customization via configuration files and generating INSDC-compliant DDBJ submission files.
• DFAST Quality Control (DFAST_QC) Quality assessment and taxonomic identification tool for prokaryotic genomes with taxonomy check using ANI against reference genomes, completeness check via CheckM, and GTDB taxonomy assignment.
• MicrobeDB.jp Integrated database for microbial genome and metagenome data combining life sciences and earth sciences data for analyzing microbial evolution and Earth-life co-evolution at the genome level.
• CRISPRdirect Rational design tool for CRISPR/Cas9 guide RNA target selection providing web-based and API-based access for designing CRISPR targets.
• PZLAST Ultra-fast amino acid sequence similarity search server against public metagenomes enabling rapid protein sequence comparison against large metagenomic databases.
• Maser One-stop platform for NGS (Next Generation Sequencing) data analysis providing integrated bioinformatics tools for sequencing data processing.
• NIG Mouse Genome Database (NIG_MoG2) User-friendly mouse genome database providing genomic information for laboratory mouse strains including the JF1 strain.
• VITCOMIC2 Fast and accurate taxonomic assignment tool for metagenomic data analysis.
• DNA Data Bank of Japan (DDBJ) One of the three major nucleotide sequence databases worldwide (with NCBI/GenBank and ENA), providing official genome data submission, annotation, and bioinformatics services.
• NIG Supercomputer System High-performance computing infrastructure at NIG providing computational resources for genomics and bioinformatics research.
• NIG-JOINT Publicly-funded collaborative research and research meeting program offering joint research opportunities for external researchers through application.
• NIG Method Scientific presentation training curriculum teaching effective English scientific communication skills, including Oral Scientific Communication courses offered to researchers across institutions.
• Integrated Research Core (NIGiRC) Core research facility comprising Advanced Genomics Center, Data Analysis Center, Genetic Resource Center, and Phenotype Research Center providing shared research infrastructure.
• XMRs (Thing/Plant/Food Metabolome Repository) Family of comparable untargeted metabolome databases including FoodMR, PlantMR, and ThingMR for analyzing sample-specific unknown metabolites across various sample types.
• PZLAST-MAG Comprehensive genome analysis platform for metagenome-derived genomes enabling ultra-fast protein sequence similarity search against MAGs.
• Microbiome Datahub Integrated database that collects and organizes metagenome-derived genomes for microbiome research.
• AutoFixMark High-precision prediction tool for identifying CO2 fixation pathways in chemolithoautotrophic bacteria directly from genome sequences.
• M-AB Zebrafish Inbred Strain Novel zebrafish inbred strain established through full sib-pair mating for over 20 generations, providing genetically uniform model organism distributed as a bioresource.
• Zebrafish Sperm Storage Method In vitro storage method for functional zebrafish and medaka sperm at room temperature, allowing sperm survival for up to 28 days while maintaining fertility.
• i-GONAD Method

Segments3 records

Ideal customer profiles3 records

Technology focussed Yes

API detail

Has API

Yes

API docs

API detail

Core technology

AI maturity

App detail

AI capability3 records

Feature11 records

Partnerships

Eight partnerships are on record, tiered major and core.

• Miharu Town, Fukushima PrefecturemajorStrategic or Co-development Partner · 2 April 2026Signed comprehensive partnership agreement for genome analysis of the national natural monument 'Miharu Takizakura' (waterfall cherry tree), estimated to be 1000 years old. Collaboration for cherry tree conservation research.
• Research Organization of Information and Systems (ROIS)coreStrategic or Co-development PartnerNIG is one of four national research institutes comprising ROIS, which also includes National Institute of Polar Research, National Institute of Informatics, and Institute of Statistical Mathematics. ROIS provides shared infrastructure and collaborative framework for inter-university research.
• National BioResource Project (NBRP)coreStrategic or Co-development PartnerNIG serves as a core facility for NBRP, which collects, preserves, and distributes biological resources including mouse strains, plants, and microorganisms for research use in Japan.
• DNA Data Bank of Japan (DDBJ)coreTechnology or IntegrationNIG houses and operates DDBJ, one of the three major nucleotide sequence databases worldwide (with NCBI/GenBank and ENA). Provides genome annotation and submission services.
• RIKEN BioResource Research Center (BRC)majorStrategic or Co-development PartnerCollaborates with RIKEN BRC on mouse resource development and genome database integration, particularly for wild mouse strain resources.
• Database Center for Life Science (DBCLS)majorTechnology or IntegrationCollaborates with DBCLS on integrated database development and bioinformatics tool integration for life science research.
• Forestry and Forest Products Research InstitutemajorStrategic or Co-development PartnerCollaborated on Sakura 100 Genome Consortium project for cherry blossom genome analysis, successfully decoding the complete genome of Ooshima cherry blossom.
• Kyowa Kirin Co., LtdmajorStrategic or Co-development PartnerJoint research collaboration on efficient production of recombinant proteins using Tol2 transposon system in suspension CHO cells.

Scale indicators3 records

Recent moves7 records

Expansion highlights5 records

Broad incumbents

• Broad Institute of MIT and Harvard: Operates major genomics and computational biology programs with strong ties to the global research community. While US-based and more commercially oriented than NIG, Broad's combination of research, tools (e.g., GATK), and infrastructure parallels NIG's integrated model.
• Wellcome Sanger Institute: UK-based genomics and biodata institute with similar research scope (genome sequencing, model organism biology, bioresources). Although funded primarily by Wellcome rather than government, Sanger shares NIG's model of combining cutting-edge research with public database provision.
• Joint Genome Institute (JGI, DOE): US Department of Energy user facility for integrative genomic science, providing high-throughput sequencing and computational analysis. Comparable to NIG in offering shared infrastructure and tools to the broader research community.

Direct peers

• European Bioinformatics Institute (EMBL-EBI): Operates the European Nucleotide Archive (ENA), one of DDBJ's two sister INSDC databases. EMBL-EBI is the most direct functional peer: a publicly funded institute providing genomics databases, bioinformatics tools, and computational infrastructure to the global research community.
• RIKEN (Institute of Physical and Chemical Research): Japan's flagship national research institute covering multiple disciplines including life sciences, with which NIG collaborates on bioresources (RIKEN BRC). Both operate under MEXT with comparable mandates and infrastructure scale, making RIKEN the closest domestic peer.
• Beijing Institute of Genomics (Chinese Academy of Sciences): China's national genomics institute conducting large-scale genome sequencing, bioinformatics database development, and population genomics. Operates under CAS as a national-level research body analogous to NIG's MEXT mandate.
• SIB Swiss Institute of Bioinformatics: Swiss national bioinformatics institute providing databases, tools, and computational resources to the life sciences community. Operates under a public-mandate model analogous to NIG, including shared infrastructure provision to academic users.
• National Center for Biotechnology Information (NCBI/NIH): Operates GenBank, the third member of the INSDC alongside DDBJ and ENA. NCBI is the largest publicly funded bioinformatics institute globally and the most direct peer in terms of mandate, scale, and function.

Regional players

• Korea National Institute of Biological Resources (NIBR): Korea's primary bioresource collection and bioinformatics facility. Shares NIG's mandate for biological resource preservation and genetic research infrastructure, but operates at smaller scale within a single national context.
• Genome Institute of Singapore (GIS, A*STAR): Singapore's flagship genomics institute conducting population and clinical genomics with government backing. Comparable to NIG's research scope but operating at smaller scale in a different national context.

Market position

Strengths5 records

Weaknesses5 records

Competitive moat6 records

Key risks5 records

Key highlights6 records

Customer concentration

• Xx.com/NIG_idenken
• LinkedInlinkedin.com/company/national-institute-of-genetics-japan
• Facebookfacebook.com/profile.php

Revenue estimate

Valuation estimate

Number of profiles

Profiles1 record

Funding overview

Funding rounds

Investors

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M&A

Investments

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