CENG 4217 — Bioinformatics Algorithms
General Information
| Field | Details |
|---|---|
| Semester | Fall 2025–2026 |
| Instructor | Arda Söylev (asoylev@erbakan.edu.tr) |
| Teaching Assistant | Elif Uysal (elif.uysal@gidatarim.edu.tr) |
| Office Hours | To be announced (by appointment) |
| Class Hours | Tuesday, 10:00 – 13:00 (MB-101/102) |
| Textbooks | - Phillip Compeau & Pavel Pevzner, Bioinformatics Algorithms: An Active Learning Approach, 3rd Edition (Recommended) - Neil C. Jones & Pavel A. Pevzner, An Introduction to Bioinformatics Algorithms (Computational Molecular Biology), MIT Press, 2004 (Recommended) - Genome-Scale Algorithm Design: Bioinformatics in the Era of High-Throughput Sequencing, Cambridge University Press, 2023 (Recommended) |
Announcements
- 08.09.2025 — All course-related announcements will be posted here.
Course Schedule
| Week / Date | Topics | Reading | Slides |
|---|---|---|---|
| 1 16.09.2025 |
Introduction Molecular biology foundations Algorithm complexity overview |
— | Slides 1 |
| 2 23.09.2025 |
DNA patterns Frequent patterns Motifs |
— | — |
| 3 30.09.2025 |
String matching Z-algorithm, Knuth–Morris–Pratt, Boyer–Moore Simple indexing, approximate matching |
— | — |
| 4 07.10.2025 |
Alignment Similarity (Hamming distance, edit distance) Dynamic programming: global and local alignment |
— | — |
| 5 14.10.2025 |
Read Alignment Trie Suffix trie Suffix tree Suffix array |
— | — |
| 6 21.10.2025 |
Paper Presentations | — | — |
| 7 28.10.2025 |
Burrows–Wheeler Transform (BWT) and FM-index Multiple sequence alignment |
— | — |
| 8 04.11.2025 |
Assembly Overlap–Layout–Consensus (OLC) De Bruijn graphs Error correction |
— | — |
| 8–16 Nov. | Midterm Exam | — | — |
| 9 18.11.2025 |
Clustering K-means Expectation–Maximization (EM) |
— | — |
| 10 25.11.2025 |
Unix tools Bash, AWK, SED |
— | — |
| 11 02.12.2025 |
Hidden Markov Models (HMMs) | — | — |
| 12 09.12.2025 |
Phylogeny | — | — |
| 13 16.12.2025 |
K-mers - Bloom filters - Sketching - Minimizers - MinHash Metagenomics |
— | — |
| 14 23.12.2025 |
Project Presentations | — | — |
Evaluation and Grading
- Midterm (40%)
- Paper Presentation: 20%
- Midterm Exam: 20%
- Final (60%)
- Project: 30%
- Proposal: 5%
- Implementation and Final Report: 15%
- Presentation: 10%
- Final Exam: 30%
- Project: 30%
Attendance
According to university regulations, students are required to attend at least 70% of the lectures. Those falling below this threshold will automatically fail the course.
Grading Policy
No individual discussions will be held regarding grades.
Requests concerning passing grades, exam performance, or appeals for course completion will not be answered. Such messages will be disregarded.
Academic Integrity
Any form of cheating, plagiarism, or academic dishonesty is considered a serious violation.
- Students caught cheating, facilitating cheating, or attempting to cheat will be subject to disciplinary action under university regulations.
- In such cases, the exam or assignment will receive a grade of zero (0) and the incident will be reported to the relevant authorities.