BioDX

BioDX

Collaborative bioinformatics services for genome analysis of organisms used in industry

BioDX

About BioDX

BioDX (Bio-Digital Transformation) combines biotechnology with digital technology to move industrial research and development forward. PtBio uses this approach to help companies across many industries make use of biological resources.

Genomic analysis of organisms used in industry, such as fermentation microbes, crops, and aquatic species, can present challenges that differ from those of model organisms: there may be no reference genome, the genome may be polyploid, and annotation may be limited. PtBio understands these problems and offers collaborative custom analysis, designing the analysis strategy together with you.

Value

The Value of PtBio's BioDX

PtBio's BioDX uses genome data and bioinformatics analysis to help you make timely, informed R&D decisions. Efficient experimental design and analysis cut unnecessary experiments and reduce costs.

Genomic data from untapped biological resources can open new markets and lead to new products. We also contribute to sustainability by helping develop varieties adapted to their environment and bio-based materials.

Through our collaboration with Hiroshima University, we turn university research into practical applications that help you build competitive products and services.

Reasons

Five Strengths of PtBio's BioDX

  1. 01

    Collaborative custom analysis

    We do not stop at delivering data. PtBio designs the analysis around your organism and goal and supports you through interpretation and the next steps. Support continues after delivery, with additional analyses and help setting up an analysis environment.

  2. 02

    Joint research lab at Hiroshima University

    PtBio runs a joint research laboratory with Hiroshima University: the Laboratory of Bio-DX (Professor Hidemasa Bono, Graduate School of Integrated Sciences for Life). We apply methods developed at the university to organisms used in industry to draw out findings a standard approach would miss.

    Through this joint research we bring in genome assembly and annotation methods, genome-based databases such as GTDB (Genome Taxonomy Database), and analysis pipelines tuned to organisms used in industry.

  3. 03

    Track record with industrial organisms

    PtBio has built its experience on organisms used in industry rather than model organisms: filamentous fungi, yeasts, bacteria, and microalgae among microorganisms; grains, vegetables, fruit trees, and seaweed among plants; and fish and laboratory animals.

    We apply what we have learned from the genomes of organisms used in industry to the experimental design and choice of methods for your next project.

  4. 04

    Read types chosen for your goal

    We use long reads (PacBio HiFi) or short reads depending on the goal. Long reads are for de novo assembly, Iso-Seq (full-length isoform sequencing), and full-length 16S rRNA amplicon analysis. Short reads are for variant analysis and RNA-seq (RNA sequencing).

    For phylogenetic data across many samples, we add GRAS-Di, a low-cost genotyping method (sequencing outsourced).

  5. 05

    One-stop service

    We handle everything from DNA and RNA extraction through analysis and reporting. Sample shipment, nucleic acid extraction, library preparation, sequencing, analysis, reporting, and ongoing support all run through a single contact.

    You send us the biological samples, and we handle the rest, from consulting on experimental design to interpreting the data and proposing next steps.

Publications

1. Tamura K, Sakamoto M, Tanizawa Y, Mochizuki T, Matsushita S, Kato Y, et al. A highly contiguous genome assembly of red perilla (Perilla frutescens) domesticated in Japan. DNA Res. 2023;30(1):dsac044. https://doi.org/10.1093/dnares/dsac044

2. Nakamae K, Bono H. Genome editing and bioinformatics. Gene and Genome Editing. 2022;3–4:100018. https://doi.org/10.1016/j.ggedit.2022.100018

3. Toga K, Sakamoto T, Kanda M, Tamura K, Okuhara K, Tabunoki H, et al. Long-read genome assembly of the Japanese parasitic wasp Copidosoma floridanum (Hymenoptera: Encyrtidae). G3 (Bethesda). 2024;14(8):jkae127. https://doi.org/10.1093/g3journal/jkae127

4. Nakamae K, Bono H. DANGER analysis: risk-averse on/off-target assessment for CRISPR editing without a reference genome. Bioinform Adv. 2023;3(1):vbad114. https://doi.org/10.1093/bioadv/vbad114

5. Nakamae K, Kakuzaki T, Yamamoto K. Machine learning of transcriptome data treated with DNA base editor. Preprint. 2023. https://doi.org/10.37044/osf.io/zytkj

6. Nakamae K, Ide S, Ohnuki N, Nakagawa Y, Okuhara K, Bono H. PtWAVE: a high-sensitive deconvolution software of sequencing trace for the detection of large indels in genome editing. BMC Bioinformatics. 2025;26(1):114. https://doi.org/10.1186/s12859-025-06139-8

7. Nakamae K, Bono H. Workflow for Fine-Tuning and Evaluating DNA Language Models for Specific Genomics Issues. Bio Protoc. 2026;16(8):e5676. https://doi.org/10.21769/BioProtoc.5676

Services

Our Services

In the initial consultation we ask about your research goal, organism, and budget, and propose a sequencing strategy and analysis plan. Questions such as "Can you do this?" or "What would it cost?" are welcome. See the individual service pages for details, or reach us through the contact page.

Contact