A small software pipeline for the discovery of potentially new ECF σ factors and the prediction of their functionality with regards to the new classification schema (Casas-Pastor et al.).

Please install hmmer 3. Furthermore, you need to install the following python packages

# requirements.txt numpy biopython==1.78 

python3 -m pip install -r requirements.txt

You can install ecf_classify with the ruby package manager

gem install ecf_classify

Add this line to your application's Gemfile:

gem 'ecf_classify'

And then execute:

$ bundle 

Or install it yourself as:

$ bundle install $ rake install 

ecf_classify commands: ecf_classify --version # print the version ecf_classify groups [FILE] # Classifies protein sequences into ECF groups ecf_classify help [COMMAND] # Describe available commands or one specific command ecf_classify subgroups [FILE] # Classifies protein sequences into ECF subgroups Options: -h, [--help], [--no-help] 

Usage: ecf_classify groups [FILE] Options: -p, [--probabilities=PROBABILTIES] -h, [--help], [--no-help] Classifies protein sequences into ECF groups 

Usage: ecf_classify subgroups [FILE] Options: -p, [--probabilities=PROBABILTIES] -h, [--help], [--no-help] Classifies protein sequences into ECF subgroups 

After checking out the repo, run bin/setup to install dependencies. Then, run rake spec to run the tests. You can also run bin/console for an interactive prompt that will allow you to experiment.

To install this gem onto your local machine, run bundle exec rake install. To release a new version, update the version number in version.rb, and then run bundle exec rake release, which will create a git tag for the version, push git commits and tags, and push the .gem file to rubygems.org.

Bug reports and pull requests are welcome on GitHub at https://github.com/r-mllr/ecf_classify.

Please cite:

Casas-Pastor D, Müller RR, Jaenicke S, Brinkrolf K, Becker A, Buttner MJ, Gross CA, Mascher T, Goesmann A, Fritz G. Expansion and re-classification of the extracytoplasmic function (ECF) σ factor family. Nucleic Acids Res. 2021 Jan 4:gkaa1229. doi: 10.1093/nar/gkaa1229. Epub ahead of print. PMID: 33398323.

The gem is available as open source under the terms of the GPL-3.