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:false ]

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

amps_faa

meta:map

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

*.faa:file

File containing AMP predictions in amino acid FASTA format

*.{faa}

amps_tsv

meta:map

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

*.tsv:file

File containing AMP predictions in TSV format

*.tsv

versions

versions.yml: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
Ask a question on Slack Open an issue on GitHub