VCU Bioinformatics and Bioengineering Summer Institute
Alignment of Pairs of Sequences
Questionnaire

Part I: Basic information

Your name 

Part II: The Scenario (using Blast)

1. Did you manage to run the programs that are part of the Scenario (i.e. BLAST/TIGR and BLAST-two-sequences/NCBI)? 

2. If so, did BLAST manage to find Primer #2R in the E. coli K12 genome? 

3. Any other comments on this section? 

Part III: Different ways of aligning sequences

4. How do you feel about your understanding of how dot matrices (or dot plots) work? 

5. Any other comments on this section? 

Part IV: The Smith-Waterman algorithm

5. Do you have a good grasp of what the Smith-Waterman algorithm is trying to accomplish?  

6. Do you feel competent in using scoring parameters to score an isolated alignment, such as the one below? 

   AAGATA--CCTACA
   |||||  |||| |
  TTAGATAAGCCTAGAG

7. How comfortable are you with the prospect of calculating a scoring table from scratch? (never mind the tedium) 

8. Would you like to see any of SQ 1-6 covered? Any other comments on this section?

Part V: Word-based algorithms

8. Comfortable with the difference between Smith-Waterman and Blast? 

9. Do you understand the significance of each of the three sets of colored boxes in Figure 4?  

10. Would you like to see any of SQ 7-8 covered? Any other comments on this section?

 

Part V: Miscellaneous

11. Other comments, concerns, questions? 

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