SegMantX

SegMantX identifies diverged segmental duplications in prokaryote genomes using local alignment chaining.

Key Features:

• Diverged duplication detection: Detects segmental duplications beyond the sensitivity limits of standard alignment-based methods by chaining local alignments into continuous segments.
• Local alignment chaining: Chains local alignments from preliminary sequence similarity searches (e.g. BLASTn) into continuous segments to reconstruct diverged duplications.
• Gene transfer identification: Identifies diverged gene transfers between replicons and plasmid hybridization events.

Scientific Applications:

• Plasmid evolution research: Applied to 6,784 enterobacterial plasmids to reveal that 65% contain duplicated regions and gene duplications, most corresponding to dispersed noncoding regions or duplicated mobile genetic elements (MGEs; e.g. transposons and insertion sequences).
• Mobile genetic element analysis: Highlights MGEs as drivers of segmental duplications in plasmid evolution, leading to amplification of cargo genes including antibiotic resistance genes.
• Alignment problem reconstruction: Provides a framework for reconstructing diverged segmental duplications and other alignment problems.

Methodology:

SegMantX performs a preliminary sequence similarity search (e.g. BLASTn) to generate local alignments, then chains these local alignments into continuous segments.