We learnt how to assemble DNA fragments from a recently published N. meningitidis outbreak study using SKESA 🧬, practiced using BLAST for species identification and MLST for strain typing, and explored how serogroups are determined using specialized Python tools for capsule characterization 🔬 - such a fun and exciting hands-on introduction to genomic analysis!
Ever wondered how DNA alignment actually works under the hood? 🧬 We coded the Needleman-Wunsch algorithm from scratch, working through scoring matrices by hand with simple examples like “CAT” vs “CT” before testing on real E. coli sequences. Pretty neat to see the magic happen! ✨
🧬🔬 Explore phylogenetic analysis from genome to tree! Basic workflow with R/Bioconductor. Learnt to work with large genomic dataset. Extract 16S rRNA from 10K+ E.coli strains using dataset dehydrate, barrnap for extraction, rapidNJ for tree building & FigTree for visualization.
Instead of flashcards, we Rube Goldberg’d this with Bioconductor! Analyzed 3,280 E. coli genomes from NCBI, detecting ESBL genes in 84.4% of samples. CTX-M-15 was most common. Helped us understand gene nomenclature and sequence analysis! 📊🔬
Learn how to build a flash-card style question bank using Google Sheets as storage, R’s Plumber API, and host it on a Digital Ocean droplet—step-by-step setup, deployment, and tips.