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

# 1) Basic conversion
ct2db structure.ct > structure.db.fa

# 2) Remove pseudoknots during conversion
ct2db --no-pk structure.ct > structure_no_pk.db.fa

# 3) Override the FASTA header
ct2db --fasta-header sample_01 structure.ct > sample_01.db.fa

Recommended Workflow

1. Confirm the input really is a .ct connectivity-table file.
2. Decide whether you need pseudoknot removal or replacement of modified bases before export.
3. Convert to extended FASTA and inspect both the sequence and dot-bracket lines.
4. 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.