Refining boundaries of genomic island

speaker: Lu Bing Xin event: RAS group meeting

review paper by Lu and Leong: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4887561/

genomic island is genomic region acquired via lateral gene transfer

several mechanisms of lateral gene transfer: conjugation, transduction, etc

GI are crucial for microbial genome evolution and adaptation of microbes to the environment

• pathogenesis
• antimicrobial resistance

GI have different GC content from the core genome

methods based on sequence composition

• window based methods
• recursive segmentation

AlienHunter uses HMM to refine the boundary found from window based method