PhaMMseqs: a new pipeline for constructing phage gene phamilies using MMseqs2.

Area of Science:

• Microbiology
• Bioinformatics
• Genomics

Background:

• Phage genomes exhibit high diversity and mosaicism, complicating phylogenetic and comparative analyses.
• Lack of universally conserved genes and numerous unknown-function ORFs present significant challenges.
• Assembling related genes into 'phamilies' (phams) simplifies phage genomics and visualizes genome mosaicism.

Purpose of the Study:

• To introduce PhaMMseqs, a computationally efficient Python package for phage gene family (pham) assembly.
• To evaluate optimal parameters for pham assembly using MMseqs2.
• To facilitate the integration of newly sequenced phage genomes into existing genomic datasets.

Main Methods:

• Utilized the MMseqs2 algorithm for efficient sequence similarity searches and pham clustering.
• Developed the Python package PhaMMseqs for automated pham assembly.
• Integrated PhaMMseqs with pdm_utils for genome data management and analysis.

Main Results:

• PhaMMseqs demonstrates efficient pham assembly with modest hardware requirements.
• Key parameters for optimal pham assembly of related proteins were identified and evaluated.
• The package facilitates genome entry and data export for evolutionary and mapping analyses.

Conclusions:

• PhaMMseqs provides an efficient solution for assembling phage gene families, addressing the challenges of phage genome diversity.
• The tool supports the integration of new phage genomes, crucial for ongoing genomic research.
• PhaMMseqs aids evolutionary analyses and phage genome map construction, advancing comparative phage genomics.