kinwalker

name	kinwalker
description	Use when simulating RNA folding kinetics during transcription to predict cotranscriptional folding pathways and transient intermediate structures.
disable-model-invocation	true
user-invocable	true

kinwalker

Quick Start

• Command: kinwalker [OPTIONS] < SeqFile > Outfile
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/kinwalker
• Full reference: references/help.md

When To Use This Tool

• Model cotranscriptional RNA folding while the chain is still elongating.
• Compare different barrier heuristics for transient folding pathways.
• Tune transcription rate and folding window size to match a biological regime.
• Produce a trajectory-oriented kinetics prediction rather than an equilibrium ensemble.

Common Patterns

# 1) Run a basic cotranscriptional folding simulation
kinwalker < seq.txt > trajectory.txt

# 2) Change the barrier heuristic and transcription rate
kinwalker --barrier_heuristic B --transcription_rate 50 < seq.txt > trajectory.txt

# 3) Constrain the folding window and disable lonely pairs
kinwalker --windowsize 120 --nolonely 1 < seq.txt > trajectory.txt

Recommended Workflow

1. Prepare sequence input file with target RNA sequence
2. Select barrier heuristic via --barrier_heuristic (M/S/B/A; default: M for Morgan-Higgs)
3. Set transcription parameters (--transcription_rate, --transcribed, --windowsize) to match biological conditions
4. Run kinwalker, redirect output to file, and review predicted folding trajectory

Guardrails

• Does not support --version; use --help to verify installation
• Input read from SeqFile or stdin; output written to Outfile or stdout
• ViennaRNA parameters (--dangle, --nolonely) should be consistent with any upstream/downstream ViennaRNA tools