CS 6333

Algorithms in Computational Biology

Fall 2011


The principles of algorithm design for biological datasets, and analysis of influential problems and techniques. Biological sequence analysis, gene finding, RNA folding, protein folding, sequence alignment, genome assembly, comparative genomics, phylogenetics, clustering algorithms.

Topics covered

  • Introduction to Molecular Biology.
  • Exact pattern matching algorithms.
  • Suffix trees, longest common substring.
  • Sequence alignment, dynamic programming, longest common subsequence, longest increasing subsequence.
  • Sequence assembly.
  • Gene finding.
  • Phylogeny.
  • Protein folding.
  • Clustering algorithms.

The books are not required. Some materials will be provided in class.

There will be no final exam. Projects and their presentations will be instead.