01 / Signal
PSeq Clear-Signal
Architecture™
Full-length 5′–3′ isoform reconstruction, including UTRs, constrained by reads assigned to each captured molecular template.
Phased sequencing / PSeq™
Turning RNA into full-length, isoform-resolved insight—at scale
Quantitative, isoform-level outputs designed for downstream ML models—from the short-read instruments you already use.
5′–3′full-length RNA
NGSinstrument compatible
MLmodel-ready features
The discovery layer
Phaeno's PSeq™ maps the molecular phenotype.
Gene-level counts compress biology. Isoforms capture splicing, promoter usage, UTR variation, and transcript-specific regulation—often the true functional drivers.
PSeq reveals the biological drivers obscured by gene-level summaries and incomplete isoform resolution.
PSeq Clear-Signal
02 / Molecules
A more direct view of individual isoforms
With sufficient depth and coverage, molecule-assigned reads support isoform-level measurement without reconstructing structure from pooled fragments.
03 / Workflow
Automated, molecule-aware processing
Preprocessing and quality control prepare reads for molecule-specific assignment before transcript assembly.
04 / Intelligence
Built for downstream machine learning
Structured, molecule-level features preserve isoform detail for use in ML models and established analysis tools.
From reads to resolved biology
See how PSeq chemistry and software recover complete RNA molecules on standard NGS platforms.
- Rare isoform sensitivityat <0.01% abundance
- >87%
- Full-length isoform recovery
- >94%
- Hands-on time per sample
- <2 hrs
- Library-to-FASTA turnaround
- <24 hrs
How PSeq compares
Preliminary performance data against standard short-read and long-read workflows.
| Metric | PSeq | Short-Read NGS1 | Long-Read2 |
|---|---|---|---|
| Isoform resolution | Yes | No | Yes |
| Full UTR resolution | Yes | No | partial only |
| Full-length isoform structure | molecule-constrained | inferred from pooled fragments | Yes |
| Pri-/pre-miRNA3 | Yes | fragmented/inferred | longer pri-/pre-miRNA only |
| Mature miRNA | validation pending | requires small-RNA library | No |
| Quantitative | molecule-counting | semi-quantitative | semi-quantitative |
| Direct cloning | Yes | No | No |
| Simple workflow | Yes | multi-step & model-dependent | No |
| NGS-compatible | Yes | Yes | No |
| Designed for downstream ML | Yes | No | No |
| Rare isoform sensitivity4 | >87% | <5% | ~45% |
| Full-length recovery rate | >94% | ~72% | ~88% |
| Hands-on time per sample | <2 hrs | ~3 hrs | ~6 hrs |
| Turnaround (library→FASTA) | <24 hrs | ~26 hrs | ~72 hrs |
1 Illumina TruSeq Stranded mRNA, STAR + RSEM quantification (v2.7). 2 PacBio Iso-Seq3, SMRT-Link v11, consensus polishing. 3 miRNA precursors are long enough for standard transcript-oriented workflows, although short-read data may require reconstruction. Mature miRNAs are approximately 22 nt and require efficient small-RNA capture. 4 Rare isoforms are <0.01% abundance.
All data are for research use only (RUO); not validated for clinical diagnostics.
Ready to resolve your samplesdown to the isoform?