CSCI3220 Algorithms for Bioinformatics - CUHK Course Review

Term Taken: 2019 Fall

Instructor: Prof. Kevin Yip Yuk Lap

Grading Scheme

Original Scheme:

  • Assignments (45%)
  • Ureply Quiz (5%)
  • Midterm Exam (20%)
  • Final Exam (30%)

Scheme for 2019 Course Cancellation:

  • Assignments (54%)
  • Ureply Quiz (6%)
  • Midterm Exam (40%)

Topics Covered

  • Optimal sequence alignment.
  • Heuristic sequence alignment (BLAST/FASTA).
  • Short read alignment (Suffix Trie, BWT).
  • Sequence assembly (de Bruijn graph).
  • Sequence motif models, k-mer counting.
  • Hidden Markov models.
  • Phylogenetic tree reconstruction.
  • Genetic data inference.
  • Clustering algorithms.
  • RNA secondary structure prediction.


This course is a combination of biology and computer science, but the course materials focus on algorithms rather than biology knowledge. Namely, the gravity is on computer science rather than biology.

Many algorithms for solving bioinformatics problems are introduced, compared, and analyzed in the class. And most interestingly, almost all of the algorithms introduced are also useful outside of bioinformatics. Thus, if you are interested in the design and analysis of algorithms, this course is for you.

As for the homework, we have to implement selected algorithms using either Java, Python, C++ or C and submit it through an online judge system. It is challenging but extremely rewarding, since you would get a much deeper understanding on the algorithms once you implement them.

Prof. Yip is a great instructor, he explains everything clearly and make sure all prerequisite knowledge is taught before moving on to the algorithm itself. The lectures are extremely enjoyable and I highly recommend this course for all computer science students even if you are not into biology.

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