AMPA-NF is a pipeline for assessing the antimicrobial domains of proteins, with a focus on the design on new antimicrobial drugs. The application provides fast discovery of antimicrobial patterns in proteins that can be used to develop new peptide-based drugs against pathogens.
Make sure you have installed the dependencies required listed at the end of this document.
Install the Nextflow runtime by running the following command:
$ curl -fsSL get.nextflow.io | bash
When done, you can execute AMPA by entering the command shown below:
$ ./nextflow run cbcrg/ampa-nf
By default the pipeline is executed by using a small dataset included with the project. Check the Pipeline parameters section below to see how specify your input data on the program command line.
#####--in
- The query sequences multi-fasta file (default: example.fa)
- Example:
nextflow ampa.nf --in /some/path/your-query.fa
#####--out
- Path to the file where save the results (default: bigampa.data)
- Example:
nextflow ampa.nf --out /some/path/your-result.data
#####--t
- Threshold value (default: 0.225)
- Example:
nextflow ampa.nf --t 0.3
#####--w
- Window size value (default: 7)
- Example:
nextflow ampa.nf --w 8
- PERL
- Math::CDF
- Math::Round
- Bio::SeqIO
AMPA: an automated web server for prediction of protein antimicrobial regions