mGenomeSubtractor

mGenomeSubtractor performs mpiBLAST-based comparative genomic subtraction to identify strain-specific variable accessory regions and define species-specific gene pools by comparing a reference bacterial genome against multiple subject genomes at DNA and amino acid levels.

Key Features:

• High-Speed Analysis: Utilizes mpiBLAST and parallel computing to run rapid BLAST searches for genomic comparisons.
• Flexible Genome Fragmentation: Employs a sliding window-based fragmentation approach to segment genomes and detect short unique sequences within or between genes.
• Segmented DNA and Amino Acid Comparison: Performs segmentation and comparative analyses at both DNA and amino acid levels.
• Output Schematics: Generates schematic outputs for exploration of core and accessory regions and supports searches against databases of mobile genetic elements, virulence factors, and bacterial essential genes.
• Genomic Characterization Tools: Computes G+C content and binucleotide distribution bias for assessment of genomic composition.
• Integrated Primer Design: Performs primer and oligonucleotide design for downstream experimental applications.
• Species-Specific Gene Pool Definition: Defines species-specific gene pools based on available genomes to support targeted genomic studies.

Scientific Applications:

• Biomarker Discovery: Defines genomic biomarkers related to evolutionary lineage, phenotype, pathotype, environmental adaptation, and disease association across bacterial species.
• Pan-genome Array Design: Supports development of pan-genomic arrays using oligonucleotide design for high-throughput studies.
• Accessory Region Identification: Identifies strain-specific variable accessory regions for analyses of mobile genetic elements, virulence factors, and essential gene content.

Methodology:

mpiBLAST-based BLAST comparisons carried out on parallel computing architecture, sliding window genome fragmentation for segmentation, comparative analysis of segmented reference genomes against multiple subject genomes at DNA and amino acid levels, and database searches against mobile genetic elements, virulence factors, and bacterial essential genes with integrated oligonucleotide/primer design.