Auto Traveler
Auto Traveler automatically generates RNA secondary structure in standard layouts using templates from the following sources:
- CRW (5S and SSU rRNA)
- Rfam (>2,000 RNA families)
- RiboVision (LSU rRNA)
RNAcentral uses Auto Traveler to visualise RNA secondary structures. For more details see RNAcentral help or browse all secondary structures.
Method overview
- Generate a library of covariance models using bpseq files from CRW, RiboVision or another source with Infernal. For best results, remove pseudoknots from the secondary structures using RemovePseudoknots from the RNAStructure package.
- Select the best matching covariance model for each input sequence using Ribotyper.
- Fold input sequence into a secondary structure compatible with the template using the top scoring covariance model.
- Generate secondary structure diagrams using Traveler and the secondary structure layouts.
Installation
Pull from Docker Hub:
docker pull rnacentral/auto-traveler
or build your own Docker image:
# Get the code:
git clone https://github.com/RNAcentral/auto-traveler.git
cd auto-traveler
# Build and tag a Docker image:
docker build -t rnacentral/auto-traveler .
Usage
Run Docker container and mount the current directory inside the container:
docker run -it -v `pwd`:/rna/auto-traveler rnacentral/auto-traveler
Perform one-time initial setup:
cd auto-traveler
auto-traveler.py setup
# run tests to verify that the installation worked
python3 -m unittest
Run examples:
python3 auto-traveler.py draw examples/examples.fasta temp/examples
For performance reasons you can run the following commands:
auto-traveler.py crw draw examples/crw-examples.fasta temp/crw-examples
auto-traveler.py ribovision draw examples/lsu-examples.fasta temp/lsu-examples
auto-traveler.py rfam draw RF00162 examples/RF00162.example.fasta temp/rfam-example
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:
python3 utils/generate_cm_library.py
python3 utils/generate_lsu_cm_library.py
python3 utils/generate_model_info.py
python3 utils/generate_model_info.py --cm-library=data/ribovision/cms --rna-type=LSU