ICEscreen

ICEscreen detects Integrative and Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Firmicute genomes to annotate mobile genetic elements that carry genes associated with antibiotic resistance, virulence, and specialized metabolic pathways.

Key Features:

• Signature Protein Detection: Identifies signature proteins of ICEs and IMEs using a Firmicute-dedicated database containing manually curated proteins and Hidden Markov Model (HMM) profiles.
• Composite Structure Detection: Implements a novel algorithm to detect composite structures composed of ICEs and IMEs commonly observed in Firmicute genomes.
• Benchmarking and Validation: Benchmarks detection results against experimentally supported elements and a public dataset of 246 manually annotated elements from 40 Firmicute genomes.

Scientific Applications:

• ICE/IME Annotation: Provides precise annotation of ICEs and IMEs in Firmicute genome sequences.
• Detection of Adaptive Genes: Identifies MGEs that carry antibiotic resistance, virulence, and specialized metabolic pathway genes.
• Genome Evolution Studies: Enables studies of bacterial genome evolution and adaptation in Firmicutes.

Methodology:

Detection of signature proteins using a Firmicute-specific database of manually curated proteins and HMM profiles; identification of composite ICE/IME structures using a novel algorithm; benchmarking against experimentally supported elements and a public dataset of 246 manually annotated elements from 40 Firmicute genomes.