MobilomeFINDER

MobilomeFINDER identifies and characterizes genomic islands (mobilomes) in bacterial genomes by integrating ArrayOme and tRNAcc for high-throughput detection and analysis.

Key Features:

• Integration of ArrayOme and tRNAcc: Combines ArrayOme, which processes microarray-derived comparative genomic hybridization (CGH) data, with tRNAcc, which analyzes tRNA and tmRNA integration hotspots across genomes.
• Microarray-Visualized Genome (MVG) Construction: ArrayOme infers contigs by merging adjacent genes classified as "present" in microarray data to form an MVG and estimate genome representation by probes.
• Identification of Genomic Islands: tRNAcc automates genomic island identification by comparing the contents and contexts of tRNA and tmRNA sites across closely related sequenced genomes to pinpoint insertion hotspots.
• Design of Hotspot-Flanking Primers: Provides accessory tools to design primers flanking identified hotspots for in silico PCR and experimental validation of genomic islands.
• Graphical and Tabular Representation: Produces schematic, graphical, and tabular representations of island-specific features and genome-contextual information.

Scientific Applications:

• Comparative genomic island discovery: Applied to genomes from Enterobacteriaceae, Pseudomonas aeruginosa, Streptococcus suis, and Escherichia coli to identify and characterize genomic islands.
• High-throughput screening of unsequenced strains: Uses microarray-derived CGH and MVG versus physical genome size discrepancies to flag strains with potential novel genes for targeted PCR and sequencing.
• Gene discovery and mobilome profiling: Enables gene discovery studies and profiling of the global gene pool accessible to individual bacterial species using emerging sequence data and PCR-based profiling.

Methodology:

ArrayOme calculates genome representation by microarray probes and constructs MVGs by merging adjacent "present" genes; tRNAcc performs MAUVE-facilitated multigenome comparisons to examine tRNA and tmRNA contexts and identify islands; in silico PCR based on conserved flanking regions is used to interrogate hotspots.