You may choose to work through any of the following exercises at your own pace for the remaining time of your session. You will need to open the NCBI home page in a second browser window, reserving this window for the exercise directions. Click here to open this second window, then return to this window and select an exercise.

The exercises are listed in order of increasing complexity. Each exercise page consists of several numbered steps, each with a checkbox that you can check to mark your progress.

• Basic Exercises
  • 1. Finding a Structural Template for an Unannotated Protein
    • Use precomputed CD-Search results and a curated CD to find a structural template and functional annotations

  • 2. Finding a Structural Template of a Gene Product
    • Use Blink and VAST to build a structural template for a gene product, and then use alignment tools in Cn3D to explore a SNP associated with a disease phenotype linked to the gene

  • 3. Finding a Structural Template for a Disordered Region
    • Use VAST to discover a template for the disordered region, and then use a curated CD to predict its function

  • 4. Structural Features Conferring Enzyme Thermostability
    • Use both BLAST and VAST to discover stabilizing features of a DNA photolyase

• Advanced Exercise
  • 5. The Alignment Challenge: An enzyme of unknown structure
    • Using both BLOCKER and the Threader, create a preliminary alignment of a novel DNA photolyase to a VAST alignment of related bacterial enzymes

Revised June 19, 2006