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

Published in: Bioinformatics (Oxford, England) (2024)

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.

Keyphrases

signaling pathway
lps induced
protein protein
nuclear factor
pi k akt
oxidative stress
binding protein
transcription factor
machine learning
electronic health record
inflammatory response
small molecule
gene expression
genome wide
immune response
rna seq
toll like receptor