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AMPA-NF

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.

Quick start

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.

Pipeline parameters

#####--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

Dependencies

• PERL
• Math::CDF
• Math::Round
• Bio::SeqIO

Cite

AMPA: an automated web server for prediction of protein antimicrobial regions