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
pi k akt
oxidative stress
protein protein
nuclear factor
amino acid
deep learning
transcription factor
machine learning
binding protein
genome wide
gene expression
toll like receptor