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Version: 0.0.1 · Java: 21 · Build system: Maven
RNA2DUnifier is a Java library that reads the output of several RNA secondary structure analysis tools and converts it into a single, unified format called extended BPSEQ. This allows downstream tools and pipelines to work with a consistent representation regardless of which tool produced the original annotation.
| Tool | Format type |
|---|---|
| FR3D | JSON |
| RNAview | Plain text |
| RNApolis | FASTA + tabular |
| mc-annotate | Plain text |
| Barnaba | Tabular annotations |
| bpnet (BPFIND) | Tabular annotations |
| x3dna-DSSR | JSON |
All interactions are classified using the Leontis–Westhof geometric nomenclature and exported to an extended BPSEQ file where each nucleotide position is associated with its pairing partners for every interaction family.
| Page | Description |
|---|---|
| Background | BPSEQ format, extended BPSEQ, and Leontis–Westhof nomenclature |
| Architecture | Package structure and component overview |
| Getting Started | Prerequisites, build instructions, and adding as a dependency |
| Quick Start | Code examples to get running immediately |
| Core API | Full reference for all public classes and methods |
| Supported Input Formats | Format details and examples for each of the seven tools |
| Output Formats | Extended BPSEQ and canonical BPSEQ output structure |
| Auto-Detection | How tool type auto-detection works |
| Logging | Configuring SLF4J / Logback |
| Error Handling | Exception types and common causes |
| Running Tests | Running the test suite |
| Advanced Usage | Streams, programmatic construction, custom exporters |
| Troubleshooting | Common issues and solutions |
RNA2DUnifier – Copyright © 2026 Francesco Palozzi.
University of Camerino – Licensed under the Apache License, Version 2.0.