15-Day Hands-On Curriculum
Click on any day below for production Biopython scripts, tool parameters, mathematical derivations, and hands-on exercises.
Day 1: Biological Databases & Programmatic Sequence Retrieval (NCBI, UniProt, PDB)
Primary vs secondary biological databases, Entrez E-utilities API, UniProtKB curated annotations, PDB atomic coordinates, and automated FASTA sequence extraction with Biopython.
Day 2: Nucleotide Composition, GC Content Analysis & Six-Frame Sequence Translation
GC percentage & isochores, sliding-window GC skew for replication origin detection, CpG island identification, and universal six-frame sequence translation.
Day 3: Open Reading Frame (ORF) Identification & In Silico Gene Prediction
Biological definition of open reading frames, NCBI ORFfinder logic, start/stop codon rules, bacterial vs eukaryotic gene architectures, and coding potential scoring.
Day 4: In Silico PCR Primer Design, Melting Temperature (Tm) & Oligo Quality Control
Thermodynamic nearest-neighbor melting temperatures, GC clamp rules, hairpin loops, primer-dimers, and in silico electronic PCR validation using Primer3 and NCBI Primer-BLAST.
Day 5: In Silico Restriction Mapping & Recombinant Molecular Cloning
Type II restriction endonucleases, palindromic cleavage geometry (sticky vs blunt), isoschizomers, directional plasmid cloning, and simulated agarose gel electrophoresis.
Day 6: In Silico Gene Editing: CRISPR-Cas9 Target Selection & sgRNA Optimization
CRISPR-Cas9 ribonucleoprotein mechanism, Protospacer Adjacent Motif (PAM) scanning, on-target efficiency scoring, off-target cleavage risk mitigation, and donor repair template design.
Day 7: Pairwise Sequence Alignment, Scoring Matrices & Heuristic Database Searching (BLAST)
Global (Needleman-Wunsch) vs local (Smith-Waterman) dynamic programming, PAM vs BLOSUM scoring matrices, Karlin-Altschul E-value statistics, and NCBI BLAST+ command line mastery.
Day 8: Multiple Sequence Alignment (MSA): Algorithms, Gap Penalties & Jalview
Progressive alignment (Clustal Omega), iterative refinement (MUSCLE), fast Fourier transform (MAFFT), affine gap penalties, conservation scoring, and Jalview visual analysis.
Day 9: Molecular Phylogenetics: Tree Construction, Evolutionary Models & Bootstrapping
Distance-based (Neighbor-Joining) vs character-based (Maximum Likelihood) phylogenetic inference, substitution models (JC69, HKY85, GTR), and non-parametric bootstrap validation.
Day 10: Conserved Protein Domain Architecture: CDD, Pfam & InterProScan
Protein domain modularity, NCBI Conserved Domain Database (CDD), Pfam Profile Hidden Markov Models (HMMER), InterPro multi-database signatures, and functional domain mapping.
Day 11: Sequence Motif Discovery & Functional Pattern Matching (PROSITE & MEME)
Deterministic regular expressions in PROSITE, ScanProsite pattern syntax, Position Weight Matrices (PWMs), sequence logos, and de novo motif discovery with the MEME Suite.
Day 12: Integrative Desktop Bioinformatics with Unipro UGENE Workbench
End-to-end desktop life science computing with UGENE: circular plasmid viewer, genome browser tracks, NGS assembly alignment viewer, and automated visual workflow designer.
Day 13: Macromolecular 3D Structure Exploration: PDB, Mol* & PyMOL Visualization
PDB/mmCIF atomic coordinate structures, crystallographic resolution, B-factors, Mol* interactive rendering, PyMOL cartoon/surface representations, and Ramachandran plot validation.
Day 14: Computational Protein Structure Prediction: Homology Modeling to AlphaFold
Comparative homology modeling (SWISS-MODEL), threading, AlphaFold 2/3 and ColabFold deep learning architecture, evoformer representations, and residue confidence metrics (pLDDT & PAE).
Day 15: Whole Genome Sequencing (WGS) Principles & Microbial Genome Analysis
Short-read vs long-read sequencing paradigms, de novo microbial assembly, contig metrics (N50, L50), bacterial structural annotation, and circular genome mapping (BRIG).