Sequence design and safety assessment for oligonucleotide therapeutics and genome editing, supported by fast sequence search.
Retrieva provides bioinformatics products for nucleotide sequence search, CRISPR guide RNA design, and the design and evaluation of oligonucleotide therapeutics. Three products, each suited to a different research goal, support drug discovery at pharmaceutical companies and research institutes.
About the Bio AI Business
Research on oligonucleotide therapeutics and genome editing requires gathering information on target genes, designing sequences, and then assessing whether a designed sequence acts on unintended genes. Each step calls for its own databases and analysis tools, and the information is scattered across them.
Retrieva's Bio AI Business provides the software behind these steps. Through the package editions of GGGenome and CRISPRdirect, both published by DBCLS, and ORIGENICS, an integrated platform for oligonucleotide drug design, we give researchers an environment where they can concentrate on the design itself.
Our products are used by oligonucleotide therapeutics teams at pharmaceutical companies, academic and public research institutes, contract testing organizations, and companies working in genome editing.
Three products
Three independent products, each with a distinct role. See each product site for full features and system requirements.
Fast, exhaustive sequence search
Accurate, exhaustive and fast similar-sequence search that runs offline, suited to the safety assessment of oligonucleotide therapeutics. Short sequences of around 20 bases are searched at speed, with support for mismatches, indels and ambiguous bases. Because it runs from a USB (SSD) device, the query sequence is never sent outside your organization.
Guide RNA design for genome editing
A package that produces the same results as the web edition published by DBCLS, running on computers inside your own organization. Design highly specific guide RNAs for the CRISPR-Cas9 system and search for candidate off-target sites.
CRISPRdirect product site
launch
An integrated platform for oligonucleotide drug design
From target gene exploration through design and evaluation in one place. ORIGENICS supports target gene analysis, sequence comparison and safety assessment together, automating the collection of information that would otherwise span scattered databases and separate tools. Off-target effects are predicted as you design.
ORIGENICS product site
launchProduct comparison
The CRISPRdirect package edition and ORIGENICS both include the GGGenome package edition. Pricing and delivery options are provided individually.
Find a product by goal
You do not need to know the product names. Start from what you want to do in your research.
I want to investigate target genes and transcripts
I want to design siRNA or antisense oligonucleotides (ASO)
I want to search for similar sequences and off-target candidates
I want to design CRISPR guide RNAs
The CRISPRdirect package edition and ORIGENICS both include the GGGenome package edition.
Technology and strengths
Fast nucleotide sequence search
For short sequences of around 20 bases, similar sequences including mismatches and indels are enumerated exhaustively. Because the search runs offline, confidential sequences can be analyzed without leaving your organization.
Sequence design and off-target analysis
siRNA and antisense design, CRISPR-Cas9 guide RNA design, and evaluation of candidate off-target sites for designed sequences: the steps required for safety assessment are delivered as products.
Large-scale genome and transcript data
Public databases including D3G and RefSeq are curated and bundled with the products. Optional databases and your own nucleotide sequence databases can be added as needed.
A foundation in NLP and machine learning
Retrieva is a company whose core technologies are natural language processing, machine learning and deep learning. The Bio AI Business draws on that foundation where it is genuinely useful.
GGGenome case studies and interviews
Details
chevron_rightUsing the GGGenome packaged version to evaluate off-target effects of oligonucleotide therapeutics
Secure, fast in silico analysis with no missed hits....
Details
chevron_rightAdopting the GGGenome packaged version to assess off-target risk for antisense oligonucleotides
National Institutes of Biomedical Innovation, Health...
Details
chevron_rightIntegrating the GGGenome packaged version into Genome Editing Cloud®, a cloud-based open platform for genome editing support
PtBio Inc.PtBio Inc. adopted Retrieva’s GGGenome pac...
Details
chevron_rightDeepening life science research with GGGenome, ultra-fast genome sequence search
Yuki Naito, Project Assistant ProfessorDatabase Cent...
Frequently asked questions
A selection of questions about choosing a product. For system requirements and purchasing, see the full FAQ page.
Q.
How do GGGenome, CRISPRdirect and ORIGENICS differ?
A.
GGGenome searches nucleotide sequences and detects similar sequences and candidate off-target sites.
CRISPRdirect designs guide RNAs for the CRISPR-Cas9 system.
ORIGENICS is a platform that handles everything from target gene exploration to the design and evaluation of oligonucleotide therapeutics. They are independent products with distinct roles, so you can choose according to your research goal.
Q.
Which product should I use to design siRNA or antisense oligonucleotides (ASO)?
A.
Use ORIGENICS. It designs oligonucleotide therapeutics such as siRNA and antisense while taking into account secondary structure prediction for the target site and variant information collected from ClinVar. Comparing transcripts and using multiple alignment also lets you choose shared or divergent regions to design against.
Q.
Which product should I use to design CRISPR-Cas guide RNAs?
A.
Use the CRISPRdirect package edition. It designs highly specific guide RNAs for the CRISPR-Cas9 system against the genomes of a wide range of species. Databases for more than 350 species are available for searching candidate off-target sites.
See all questions（Japanese）
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chevron_rightContact Us by Email
info_bio@retrieva.jp
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