omicscodeathon/plaskmer

Building an African Plasmid and mRNA Databank with K-mer-Based Search --- title: Plaskmer emoji: 🧬 colorFrom: blue colorTo: green sdk: streamlit app_file: scripts/app.py pinned: false --- # Plaskmer (You can put the rest of your normal README text down here...) # plaskmer Building an African Plasmid and mRNA Databank with K-mer-Based Search # Overview Africa remains significantly underrepresented in global microbial genomic databases, limiting effective surveillance of infectious diseases and antimicrobial resistance (AMR). This gap is particularly evident in high-burden diseases such as cholera, caused by Vibrio cholerae, which continues to drive recurrent outbreaks across the continent. A major driver of Vibrio cholerae evolution is horizontal gene transfer via plasmids and other mobile genetic elements, enabling rapid dissemination of virulence and antimicrobial resistance determinants. However, conventional homology-based tools often fail to detect novel or highly divergent sequences, leaving substantial genomic diversity uncharacterized. Plaskmer is an alignment-free, k-mer based bioinformatics framework designed to address this limitation by enabling reference-independent classification of plasmid and chromosomal sequences. It builds an Africa-focused plasmid and mRNA database starting with Vibrio cholerae, supporting improved genomic surveillance and AMR tracking. --- ## 🌟 Significance & Impact Traditional genomic classification relies on homology-based tools (like BLAST), which struggle with "genomic dark matter"—novel sequences that lack close relatives in existing databases. Plaskmer addresses this by focusing on the **intrinsic statistical signatures** of DNA: * **African Pathogen Surveillance:** Rapidly sort plasmids from high-burden African pathogens (e.g., *Vibrio cholerae*, *K. pneumoniae*). * **Environmental Exploration:** Identify mobile genetic elements (MGEs) in African extreme environments, such as soda lakes and thermal pans. * **Functional Genomics:** Track Open Reading Frames (ORFs) to understand how functi …