| name | ct2db |
| description | Use when converting RNA connectivity-table (`.ct`) files into extended FASTA with dot-bracket structures, optionally removing pseudoknots or modified bases. |
| disable-model-invocation | true |
| user-invocable | true |
ct2db
Quick Start
- Command:
ct2db [options] input.ct ...
- Local executable:
/home/vimalinx/miniforge3/envs/bio/bin/ct2db
- Version observed locally:
1.0
- Help:
ct2db -h
When To Use This Tool
- Convert Zuker-style
.ct connectivity tables into dot-bracket notation.
- Turn RNA structure files into an extended FASTA representation for downstream tools.
- Remove pseudoknots or normalize modified bases during conversion.
- Batch-convert one or more
.ct files with a single command.
Common Patterns
ct2db structure.ct > structure.db.fa
ct2db --no-pk structure.ct > structure_no_pk.db.fa
ct2db --fasta-header sample_01 structure.ct > sample_01.db.fa
Recommended Workflow
- Confirm the input really is a
.ct connectivity-table file.
- Decide whether you need pseudoknot removal or replacement of modified bases before export.
- Convert to extended FASTA and inspect both the sequence and dot-bracket lines.
- Keep the original
.ct file if you will need richer connectivity information later.
Guardrails
ct2db writes converted sequences to stdout.- Help and version are available as
-h / --help and -V / --version.
--filename-suffix defaults to removing .ct when deriving FASTA headers from filenames.--no-pk removes pseudoknots, which can change structure interpretation for downstream analyses.--no-modified replaces non-canonical nucleotides with N.
