BPSS: a Nextflow pipeline for Bacterial Peptide Sequence Selection to detect protein diversity

TL;DR

BPSS is a new pipeline that helps identify diverse bacterial protein variants by selecting minimal peptide sequences for detection.

Contribution

BPSS introduces an automated, efficient tool for building nonredundant databases of bacterial protein variants.

Findings

BPSS defines a minimal set of peptides to detect all variants of a target protein.

The pipeline is designed to handle high bacterial sequence variability efficiently.

BPSS is freely available with open-source code and containers for easy use.

Abstract

Sequence variability can be extremely high, particularly in bacteria due to the rapid accumulation of mutations linked to their high replication rate and environmental selection pressure, which often favors diversifying selection. For most species, there are no automated, computationally efficient tools available for constructing a nonredundant database covering the allelic variability of target proteins.

We have thus developed Bacterial Peptide Sequence Selection, a Nextflow pipeline to define a minimal list of peptide sequences for detecting all variants of a protein of interest.

All the code and containers used are freely available on Gitlab from https://gitbio.ens-lyon.fr/ciri/stapath/bpss or on Zenodo (10.5281/zenodo.16894981) under GPLv3 open-source license and DockerHub platform from https://hub.docker.com/u/stapath.

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