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{:bash}

:map

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

faa{:bash}

:file

FASTA file containing amino acid sequences

*.{faa,fasta}

model{:bash}

:string

Built-in model for AMP prediction

{precursor,mature}

min_length{:bash}

:integer

Minimum protein length for which predictions will be generated

[0-9]+

min_probability{:bash}

:float

Cut-off for AMP prediction

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

Output

name:type
description
pattern

amps_faa{:bash}

meta{:bash}

:map

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

*.faa{:bash}

:file

File containing AMP predictions in amino acid FASTA format

*.{faa}

amps_tsv{:bash}

meta{:bash}

:map

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

*.tsv{:bash}

:file

File containing AMP predictions in TSV format

*.tsv

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

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
included in
funcscan
maintainer
Github user jasmezz
get in touch
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