Description

A fast and user-friendly method to predict antimicrobial peptides (AMPs) from any given size protein dataset. ampir uses a supervised statistical machine learning approach to predict AMPs.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

faa (file)

FASTA file containing amino acid sequences

*.{faa,fasta}

model (string)

Built-in model for AMP prediction

{precursor,mature}

min_length (integer)

Minimum protein length for which predictions will be generated

[0-9]+

min_probability (float)

Cut-off for AMP prediction

[0-9].[0-9]+

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

amps_faa (file)

File containing AMP predictions in amino acid FASTA format

*.{faa}

amps_tsv (file)

File containing AMP predictions in TSV format

*.tsv
included in
funcscan
maintainer
Github user jasmezz
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

ampir
GPL v2

A toolkit to predict antimicrobial peptides from protein sequences on a genome-wide scale.

github.com/Legana/ampir cran.r-project.org/web/packages/ampir https://github.com/Legana/ampir 10.1093/bioinformatics/btaa653