Retrieva Launches 'GGGenome Package Edition Drug Discovery Basic Pack 2026' – High-Speed Nucleotide Sequence Search System for Nucleic Acid Therapeutics

Retrieva Inc. (Headquarters: Toshima-ku, Tokyo; CEO: Takuya Taguchi) has launched the 'GGGenome Package Edition Drug Discovery Basic Pack 2026,' a high-speed nucleotide sequence search system designed for nucleic acid therapeutics—novel modality drugs utilizing RNA or DNA. This 2026 edition supports RefSeq release 230 and D3G 26.03, and introduces enhanced large-scale search speed and improved exon/intron-specific search functionality, supporting efficient off-target assessment (evaluation of potential effects on non-target genes) in drug discovery research.

As research and development of nucleic acid therapeutics such as siRNA and ASO expands, the importance of high-precision off-target evaluation and safety assessment using up-to-date databases is increasing.

GGGenome is a nucleotide sequence search system that enables fast and exhaustive searches for short-sequence targets. It supports off-target assessment critical to nucleic acid drug R&D, contributing to the efficient discovery of drug candidate sequences, safety evaluation, and large-scale sequence design.

The GGGenome Package Edition provided by Retrieva allows offline use of GGGenome and is utilized by pharmaceutical companies, biotech firms, CROs, and academic institutions.

In addition to updating to the latest RefSeq release 230 and D3G 26.03 databases, this release includes enhanced search processing speed, in-memory database residency, and improved batch search functionality. These improvements further accelerate large-scale screening and nucleic acid drug design workflows for pharmaceutical and biotech companies.

Challenges in Off-Target Assessment for Nucleic Acid Therapeutics

Nucleic acid therapeutics typically target short sequences of around 20 nucleotides. Conventional general-purpose sequence search tools may miss potential off-targets when searching for sequences with mismatches or insertions/deletions.

GGGenome employs algorithms specialized for short-sequence search, enabling fast and exhaustive searches even with mismatches or gaps. The web version of GGGenome is provided by the Database Center for Life Science (DBCLS), National Institute of Genetics (https://gggenome.dbcls.jp). (Hereafter referred to as 'GGGenome Web Version' to distinguish from the package edition.)

Additionally, GGGenome integrates the 'D3G' database, which includes pre-mRNA data (RNA prior to splicing) critical for nucleic acid drug design, enabling target discovery that includes intronic regions.

Furthermore, GGGenome has been used in safety assessments for submissions to the Pharmaceuticals and Medical Devices Agency (PMDA).

※ About D3G

D3G was constructed under the AMED Genome-based Drug Discovery Infrastructure Promotion Research Project (Kawai Team, 2017–2022) and is currently maintained by the Kawaji Team's project 'Research on Infrastructure Development for Exploring Novel Drug Targets Using Genome Information' (since FY2023). Widely used in nucleic acid drug development and regulatory submissions, D3G is also searchable via the GGGenome Web Version.

https://d3g.io/

Key Features of the GGGenome Package Edition

### Offline Usability

The GGGenome Package Edition is delivered with software pre-installed on a portable SSD, enabling use in offline environments without internet connectivity. This allows secure search and analysis without transmitting sensitive information such as drug candidate data or sequence information externally.

### Relaxed Limits for Large-Scale Searches

Compared to the web version, the package edition significantly relaxes limits on search volume and duration, enabling high-load searches with large result sets.

(Examples of relaxed limits)

- Maximum result count via API: up to 10 million - Maximum internal hit count in search engine: up to 1 billion - Maximum search timeout: up to 24 hours

### Highlight Function for Genes of Interest

Users can highlight specified genes of interest within search results, enabling efficient filtering, CSV export, and visual identification. This allows rapid extraction of high-risk off-target candidate genes from large result sets.

### Batch Search Support: 'Bioret Tool'

The Bioret Tool enables batch searches across multiple queries, cross-database searches, integration of spliced and unspliced results, execution history management, and summary reporting. This supports evaluation of effects on protein-coding regions, early safety risk screening, and acceleration of large-scale candidate sequence design.

### Original Search UI (Beta)

The Original Search UI (Beta) allows users to extract search results based on transcript metadata such as gene name, CDS/UTR regions, and exon/intron regions. This enables targeted extraction of results—such as from CDS or intron regions—improving the efficiency of functional impact assessment.

Major Updates in the 2026 Edition

### Support for Latest Databases

In nucleic acid drug development and regulatory submissions, off-target assessment using updated databases is essential.

The 2026 Drug Discovery Basic Pack now supports RefSeq release 230 and D3G 26.03.

Target species include nine commonly used in drug discovery: human, mouse, rat, rabbit, cynomolgus monkey, rhesus monkey, marmoset, dog, and pig.

Figure 1: List of databases included in the 2026 Drug Discovery Basic Pack

Figure 2: Updates from RefSeq release 225 to 230

Figure 3: Updates from D3G 25.03 to 26.03

### Enhanced Search Performance

The 2026 edition introduces two new features:

- Ability to set maximum result count for searches

- Function to keep target databases resident in memory

These allow efficient control of search processing load, improved search performance on large datasets, and smoother filtering operations.

Additionally, exon/intron-specific search is now supported in batch searches.

Integration with ORIGENICS

GGGenome is also integrated with 'ORIGENICS,' an integrated platform for nucleic acid drug design.

ORIGENICS is a unified platform that supports end-to-end workflows for the design and off-target assessment of:

- siRNA

- ASO

- CRISPR-Cas gRNA

By integrating with external databases such as NCBI datasets API and ClinVar, as well as internal databases within GGGenome, ORIGENICS enables simultaneous design and safety evaluation, reducing rework in drug discovery research.

Delivery Format

The GGGenome Package Edition is delivered with software pre-installed on a portable SSD.

Future Outlook

Retrieva will continue to advance nucleic acid drug design and off-target analysis technologies, contributing to faster and safer drug discovery research.

About Retrieva Inc.

Retrieva operates under the mission 'Supporting people with AI technology,' providing enterprise AI solutions leveraging LLMs and generative AI. Through RAG and AI-powered