ACLAME

ACLAME compiles and classifies sequenced mobile genetic elements (MGEs), with emphasis on phages and plasmids, to support analysis of their genomic content and evolutionary dynamics.

Key Features:

• Comprehensive Data Collection: Compiles high-quality sequences of mobile genetic elements, incorporating data from sources including the Prophinder database to enhance phage sequence coverage.
• Multi-Level Classification: Organizes sequences at the gene/protein level into families, identifies genome-level cohesive modules of commonly shared protein families, and represents population-level reticulate evolutionary relationships as networks.
• Protein Family Annotation: Assigns manual functional annotations to families of four or more proteins using Gene Ontology (GO) and the mobile genetic element ontology MeGO.
• Analysis Tools: Provides an extended BLAST interface and tools for in-depth analysis of search results against the compiled MGE data.

Scientific Applications:

• Evolutionary Studies: Enables mapping of evolutionary relationships among MGEs to study horizontal gene transfer and microbial evolution.
• Functional Genomics: Supports identification of potential functions of newly discovered genes within MGEs through curated protein family annotations.
• Biotechnology and Medicine: Provides genomic and functional insights into phage biology and plasmid function that can inform biotechnological applications and therapeutic strategies such as bacteriophage therapy.

Methodology:

Sequences are curated from reputable databases and predicted prophages, including incorporation of Prophinder data; protein families with four or more proteins receive manual functional annotations using Gene Ontology (GO) and MeGO; evolutionary cohesive modules are identified by grouping commonly shared protein families and relationships are represented as networks.