MgCod

MgCod predicts genes and identifies intermittent stop codon recoding in phage genomes to enable accurate annotation of genomic regions that use alternative genetic codes.

Key Features:

• Identification of Recoding Regions: Identifies genomic blocks where stop codons are recoded differently from the standard genetic code, enabling detection of regions using alternative genetic codes.
• Dual-Coding and Single-Coding Gene Analysis: Distinguishes 'single-coding' and 'dual-coding' genes, noting that dual-coded blocks translate into nearly identical proteins under two alternative genetic codes and are enriched in early-stage phage genes while late-stage genes localize to single-coded regions.
• Comprehensive Genomic Scanning: Performs large-scale scans of human metagenomic contigs to detect viral contigs exhibiting intermittent stop codon recoding, including crAssphages.
• Parallel Gene Prediction and Recoding Identification: Concurrently predicts protein-coding genes and identifies the types of stop codon recoding in novel genomic sequences.

Scientific Applications:

• Viral Genome Annotation: Enables accurate annotation of phage genomes that contain regions with alternative genetic codes.
• Evolutionary Analysis of Codon Reassignment: Supports investigation of the evolutionary implications of stop codon recoding and codon reassignment in phages.
• Metagenomic Viral Discovery and Characterization: Facilitates discovery and characterization of viral contigs in human metagenomic datasets, including crAssphages exhibiting intermittent recoding.

Methodology:

Identifies genomic blocks with stop codon recoding, classifies genes as single-coding or dual-coding, concurrently predicts genes and recoding types, and scans large metagenomic contig datasets for viral contigs exhibiting intermittent stop codon recoding.