Johns Hopkins University — Genomic Data Science Specialization Module 3: Edit Distance, Assembly, and Overlaps Student: Julian Borges, MD
Implementation of genome assembly and alignment algorithms as part of the Johns Hopkins Bioinformatics specialization. Covers edit distance computation via dynamic programming, overlap graph construction for de novo assembly, and shortest common superstring approximation.
| Algorithm | Description |
|---|---|
| Edit Distance (DP) | Dynamic programming solution for global alignment scoring |
| Approximate Matching (DP) | Edit distance based approximate pattern matching |
| Overlap Detection | Suffix-prefix overlap computation for read pairs |
| Shortest Common Superstring | Greedy assembly from overlapping reads |
| De Bruijn Graph | k-mer based graph construction for assembly |
- Dynamic programming for sequence alignment
- Overlap-layout-consensus assembly paradigm
- De Bruijn graph construction and Eulerian path traversal
- Computational complexity of assembly problems
Python · Dynamic Programming · Graph Algorithms
Julian Borges, MD, MS · ORCID · Academic CV
Frontier Translational Research Lab
Department of Computer Science · Boston University · Harvard Medical School GCSRT Alumni
Julian Borges, MD, MS · jyborges@bu.edu