Turning RNA into full-length, isoform-resolved insight—at scale

Phaeno produces fully quantitative, ML-ready outputs from short-read sequencing

Phaeno's PSeq™ — The Phased Sequencing Platform

Gene-level counts compress biology. Isoforms capture splicing, promoter usage, UTR variation, and transcript-specific regulation — often the true functional drivers.

  • ✓Isoform-resolved quantification, not gene counts
  • ✓Deterministic, chemistry-anchored measurements
  • ✓ML-native feature matrices
  • ✓The discovery layer your multi-omics stack is missing

PSeq exposes the molecular phenotype of each sample, revealing biological drivers obscured by gene-level summaries and incomplete isoform resolution.

Resolved isoforms → PSeq + multi-omics →
High-quality output

PSeq Clear-Signal Architecture™ — signal-first RNA data

Full-length 5′–3′ RNA sequencing, including UTRs, without dependence on prior annotations. Uncompressed measurement of what is present, not what is expected.

Individual molecules

Individual molecules, directly measured

True molecule-level counting of every RNA, including rare and low-frequency isoforms. No inferred abundance. No statistical reconstruction.

Automated pipeline

Fully automated, annotation-independent pipeline

End-to-end isoform assembly from raw reads with no manual intervention and no reference bias.

AI-ready data

Built for machine learning from first principles

Structured, molecule-level features derived from real measurements—not averaged signals or approximations.

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Performance Metrics

  • Metric
    PSeq
    Short Read 1
    Long Read 2
  • Qualitative Metrics
  • Isoform Resolution
    PSeq
    ✔
    Short Read1
    ✖
    Long Read2
    ✔
  • Full UTR resolution
    PSeq
    ✔
    Short Read1
    ✖
    Long Read2
    ✖
    Partial only
  • Fully assembled transcripts
    PSeq
    ✔
    Every molecule is assembled (5’ to 3’).
    Short Read1
    ✖
    Fragments require statistical reconstuction.
    Long Read2
    ✔
  • Quantitative
    PSeq
    ✔
    Fully quantitative. (Molecule-counting, no inference)
    Short Read1
    ✖
    Semi-quantitative.
    Long Read2
    ✖
    Semi-quantitative.
  • Direct cloning
    PSeq
    ✔
    Short Read1
    ✖
    Long Read2
    ✖
  • Simple workflow
    PSeq
    ✔
    Short Read1
    ✔
    But multi-step & model-dependant.
    Long Read2
    ✖
  • NGS Compatible
    PSeq
    ✔
    Short Read1
    ✔
    Long Read2
    ✖
  • AI/ML optimized
    PSeq
    ✔
    Short Read1
    ✖
    Long Read2
    ✖
  • Performance Metrics 3
  • Rare4 isoform sensitivity
    PSeq
    >87%
    Short Read1
    <5%
    Long Read2
    ~45%
  • Full-length isoform recovery rate
    PSeq
    >94%
    Short Read1
    ~72%
    Long Read2
    ~88%
  • Hands-on time per sample
    PSeq
    <2 hours
    Short Read1
    ~3 hours
    Long Read2
    ~6 hours
  • Turn-around time (library to FASTA)
    PSeq
    <24 hours
    Short Read1
    ~26 hours
    Long Read2
    ~72 hours
1
Illumina TruSeq Stranded mRNA, STAR + RSEM quantification (v2.7).
2
PacBio Iso-Seq3, SMRT-Link v11, consensus polishing.
3
PSeq performance metrics are preliminary and may be refined as additional samples are evaluated under increasingly stringent validation conditions. Turnaround time reflects best-case performance at scale.
4
<0.01% abundance.
All data are for research use only (RUO). Not validated for clinical diagnostics.