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Generate rRNA secondary structure in standard layout
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blakesweeney Merge pull request #2 from RNAcentral/extract-overlap-summary
Update traveler and extract overlap count
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Readme.md

Auto Traveler

This is a tool for automatic generation of RNA secondary structure in standard CRW layouts.

Method overview

  1. Generate a library of covariance models using CRW bpseq files and Infernal. For best results, remove pseudoknots from CRW secondary structures using RemovePseudoknots from the RNAStructure package.
  2. Select the best matching covariance model for each input sequence using Ribotyper
  3. Fold input sequence into a secondary structure compatible with the template using the top scoring covariance model.
  4. Generate secondary structure diagrams using Traveler and CRW layouts.

Installation

Download a precomputed library of covariance models: https://www.dropbox.com/s/q5l0s1nj5h4y6e4/cms.tar.gz?dl=0

Uncompress it and place the folder in auto-traveler/data/cms.

# Get the code:
git clone https://github.com/RNAcentral/auto-traveler.git
cd auto-traveler

# Build and tag a Docker image:
docker build -t auto-traveler .

# Run Docker container and mount the current directory inside the container:
docker run -it -v `pwd`:/rna/auto-traveler auto-traveler

# generate extra files required by Ribotyper:
cd auto-traveler
python utils/generate_model_info.py

Usage

Run Docker container as shown above, then inside the container:

cd auto-traveler

# run traveler on all sequences from an example file:
python auto-traveler.py examples/examples.fasta example-output

# place your fasta file in a folder that is mounted in the container:
python auto-traveler.py /path/to/input.fasta /path/to/output-folder

Additional commands:

# classify example sequences using Ribotyper
perl ribotyper.pl -i data/cms/all.modelinfo.txt -f examples/pdb.fasta example-output

# to generate covariance models:
perl utils/generate_cm_library.py

Acknowledgements

Secondary structure information was downloaded from the CRW website.

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