PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore...

Area of Science:

• Genomics
• Proteomics
• Bioinformatics

Background:

• Accurate genome annotation is crucial for understanding prokaryotic biology.
• Existing annotation methods may miss novel genes and post-translational modifications.
• Proteogenomic analysis integrates proteomic data to refine genome annotations.

Purpose of the Study:

• To release a publicly available proteogenomic annotation pipeline.
• To enable improved annotation of prokaryotic genomes.
• To facilitate the discovery of novel biological elements.

Main Methods:

• Development of a proteogenomic annotation pipeline using Python and C++.
• Integration of the Makeflow engine for workflow execution.
• Redesign for parallel Linux computing environments with automated deployment features.

Main Results:

• The pipeline has been used to improve the annotation of 46 prokaryotic genomes.
• Novel genes and post-translational modifications were discovered.
• Erroneous gene annotations were corrected using proteomic mass spectrometry data.

Conclusions:

• The first public release of a proteogenomic annotation pipeline is presented.
• The pipeline enhances prokaryotic genome annotation accuracy and completeness.
• The tool is designed for easy deployment and portability across various computing environments.