PhaMMseqs

PhaMMseqs assembles phage protein sequences into sequence-related "phamilies" (phams) using MMseqs2 to enable comparative genomics and evolutionary analysis of bacteriophages.

Key Features:

• Pham assembly with MMseqs2: Uses MMseqs2 to cluster amino acid sequences into phamilies (phams) for computationally efficient pham assembly.
• Amino-acid similarity-based clustering: Constructs phamilies based on amino acid sequence similarity to group sequence- and function-related proteins.
• Python implementation: Implemented as a Python package.
• Handling of phage genomic diversity: Accounts for mosaic genome architecture, the lack of universally conserved core genes, a high proportion (~70%) of genes of unknown function, and the prevalence of small open reading frames (<500 bp).
• Integration with pdm_utils: Integrates with pdm_utils to support genome entry and dataset export for downstream analyses and phage genome mapping.
• Scalability: Supports incorporation of newly sequenced phage genomes into existing datasets.
• Resource efficiency: Provides computational efficiency compatible with modest hardware requirements.

Scientific Applications:

• Comparative genomics of bacteriophages: Reduces phage genome mosaicism to phams for cross-genome comparisons.
• Evolutionary and phylogenetic analysis: Enables evolutionary and phylogenetic studies of phage proteins and genomes.
• Functional inference: Facilitates exploration of functional relationships among proteins, including proteins of unknown function.
• Phage genome mapping and annotation: Aids construction and annotation of detailed phage genome maps.

Methodology:

Clusters amino acid sequences using MMseqs2 within a Python package and evaluates key parameters to optimize pham assembly based on amino acid sequence similarity.