Bioinformatics lecture notes
  • Introduction
  • Introduction to biology (for computer scientists)
  • Ethical considerations
  • Finding patterns in DNA
    • Introduction to pattern discovery
    • Looking for frequent k-mers
    • Leveraging biology
    • Finding genes
  • Exact string matching
    • Introduction to exact string matching
    • Semi-numerical matching
    • The Z algorithm
    • The KMP algorithm
  • Multiple sequence alignment
    • Introduction to multiple sequence alignment
    • Motif finding
  • String indexing
    • Introduction to string indexing
    • Introduction to suffix trees
    • Suffix trees: beyond the basics
    • Suffix arrays
    • The Burrows-Wheeler transform and the FM-index
  • Inexact alignment
    • Introduction to inexact alignment
    • Inexact alignment calculation with dynamic programming
    • Example: filling the dynamic programming table
    • Modeling alignment as a graph
    • Backtracking through the dynamic programming table
    • From edit distance to alignment scores
    • Local alignment
    • Exercises
  • Advanced inexact alignment
    • Gap penalties
    • Sequence alignment in linear space
    • Sequence alignment with bounded error
  • Proteomics data analysis
    • Introduction to proteomic data analysis
    • From peptides to theoretical spectra
    • Cyclopeptide sequencing
    • Dealing with errors in experimental spectra
  • Data clustering
    • Introduction to data clustering
    • K-means clustering
    • Hierarchical clustering
  • Phylogenetic analysis
    • Introduction to phylogenetic inference
    • Distance-based phylogenetic analysis
    • Trait-based phylogenetic inference
  • Sequence assembly
    • Introduction to sequence assembly
    • Graph formulations of sequence assembly
    • Finding Eulerian tours
  • Gene finding and annotation
    • Introduction to sequence annotation
    • Gene finding
    • Introduction to Hidden Markov Models
    • Taxonomic and functional annotation
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