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. 2024 Mar 29;40(4):btae175.
doi: 10.1093/bioinformatics/btae175.

POCP-nf: an automatic Nextflow pipeline for calculating the percentage of conserved proteins in bacterial taxonomy

Martin Hölzer  1
Affiliations

POCP-nf: an automatic Nextflow pipeline for calculating the percentage of conserved proteins in bacterial taxonomy

Martin Hölzer. Bioinformatics. .

Abstract

Summary: Sequence technology advancements have led to an exponential increase in bacterial genomes, necessitating robust taxonomic classification methods. The Percentage Of Conserved Proteins (POCP), proposed initially by Qin et al. (2014), is a valuable metric for assessing prokaryote genus boundaries. Here, I introduce a computational pipeline for automated POCP calculation, aiming to enhance reproducibility and ease of use in taxonomic studies.

Availability and implementation: The POCP-nf pipeline uses DIAMOND for faster protein alignments, achieving similar sensitivity to BLASTP. The pipeline is implemented in Nextflow with Conda and Docker support and is freely available on GitHub under https://github.com/hoelzer/pocp. The open-source code can be easily adapted for various prokaryotic genome and protein datasets. Detailed documentation and usage instructions are provided in the repository.

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Conflict of interest statement

None declared.

Figures

Figure 1.
Figure 1.
Pairwise POCP values from the original study of Pannekoek et al. (2016) (upper triangle) and recalculated with POCP-nf (lower triangle) of Chlamydia strains and outgroups. The average difference of percentage is 1.72% between all POCP values. Chlamydia (C.) abortus (cab), C.avium (cav), C.caviae (cca), C.felis (cfe), C.gallinacea (cga), C.ibidis (cib), C.muridarum (cmu), C.pecorum (cpe), C.pneumoniae (cpn), C.psittaci (cps), C.trachomatis (ctr), Parachlamydia acanthamoebae (pac), Simkania negevensis (sne), Waddlia chondrophila (wch), Candidatus Rubidus massiliensis (cru)
See this image and copyright information in PMC

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