ASM Education Workshop:
Teaching Bioinformatics to Undergraduates

Intro Lecture PowerPoint file

Bioinformatics Tools PowerPoint file

BioComputing for Undergrads: PowerPoint file

Exercises

• Exercise 1: Similarity searches with BLAST
  
  
• Exercise 2: Finding and Aligning Sequences
  
  
• Exercise 3: Genomes and Pathways
  
  
• Exercise 4: Protein domains and Structure

Resources

Online Bioinformatics Tools

• NCBI home of GenBank, BLAST, and lots more essential tools
  
• EMBL the European Molecular Biology Laboratory
  
• ClustalW Multiple Alignment Web Server at EBI
  
• The UCSC Genome Browser
  
• Pfam Protein domains and families (by HMM searches)
  
• ProDom Protein Domain database
  
• KEGG: The Kyoto Encyclopedia of Genes and Genomes Metabolic and Regulatory Pathways
  
• RasMol: Protein 3D Viewer
  
• PDB: Protein Data Bank (3D Protein Structures)
  

Teaching Resources

• BLAST Tutorial
• RasMol Tutorial
  
• More RasMol Tutorials
  
  
• Geospiza Bioinformatics Tutorials
  Sandra Porter, GeoSpiza Inc. (funded in part by NSF Bio-Link)
  Very basic, suitable for high school or Intro level courses.
  
  
• Biology Student Workbench
  
  • Tutorial
    
  • BioQuest Modules
    
  • NCSA archive
  
  
• Terri Attwood's Web Biocomputing tutorials:
  University College London
  • Web practical on bioinformatics
    
  • Protein sequence analysis
  
  
• Sequence Analysis on the Web
  Christian Buschking and Chris Schleiermacher
  Bielefeld University
  
  
• Online Lectures on Bioinformatics
  Hannes Luz, Max Planck Institute for Molecular Genetics
  
  
• Using Computers for Molecular Biology, Stuart Brown, NYU School of Medicine
  
• The Bioinformatics Training Resource
  
  
• Bioinformatics Education links

Selected Readings

Computing for Biologists

• Why Biologists Want to Program Computers by James Tisdall
  
• How Perl Saved the Human Genome Project by Lincoln Stein
  

Similarity & Alignment

• Similarity Searching on the Web
  
• Advanced Similarity Searching on the Web
  
• Blast on the Web
  
• Searching Sequence Databases
  
• Multiple Alignment Tools on the Web
• Phylogenetics on the Web