cbcrg/ampa-nf

Name: ampa-nf

Owner: Notredame Lab

Description: Fast automated prediction of protein antimicrobial regions

Created: 2013-08-22 16:06:16.0

Updated: 2016-07-11 16:16:13.0

Pushed: 2017-10-13 19:53:00.0

Homepage: tcoffee.crg.cat/apps/ampa/

Size: 23053

Language: Perl

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README

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