Bioinformatics Algorithms Course

Module 1: Introduction to Bioinformatics & Sequence Data

1 week

• Topics: Biological sequence formats (FASTA, FASTQ), scoring matrices (PAM, BLOSUM)

• Hands-on: Parse real DNA/RNA FASTA files and compute simple similarity scores

Module 2: Pairwise Alignment with Dynamic Programming

1 week

• Topics: Global alignment (Needleman–Wunsch), local alignment (Smith–Waterman), affine gap penalties

• Hands-on: Implement both algorithms in Python and align sample protein sequences

Module 3: Heuristic Alignment & BLAST

1 week

• Topics: BLAST algorithm overview, word-size seeding, high-scoring segment pairs (HSPs)

• Hands-on: Use Biopython to run and parse BLAST searches against a small custom database

Module 4: Multiple Sequence Alignment

1 week

• Topics: Progressive alignment (ClustalW), iterative refinement, consistency-based methods

• Hands-on: Align a set of homologous protein sequences and visualize conserved motifs

Module 5: Genome Assembly Algorithms

1 week

• Topics: Overlap–layout–consensus vs. de Bruijn graph approaches, error correction basics

• Hands-on: Build a de Bruijn graph from simulated reads and extract contigs

Module 6: Hidden Markov Models in Bioinformatics

1 week

• Topics: HMM components, Viterbi and forward–backward algorithms, profile HMMs for domain detection

• Hands-on: Train a simple HMM for gene prediction on toy bacterial sequences

Module 7: Phylogenetic Inference & Tree Reconstruction

1 week

• Topics: Distance-based (UPGMA, neighbor-joining) and character-based (maximum parsimony, maximum likelihood) methods

• Hands-on: Construct and compare phylogenetic trees from aligned sequences using scikit-bio

Module 8: Advanced Topics & Capstone Project

1 week

• Topics: Sequence clustering, variant calling basics, scalable algorithms for big data

• Hands-on: End-to-end mini-project: annotate a draft bacterial genome with gene models and variant sites

Get certificate