VCU Bioinformatics and Bioengineering Summer Institute
Sequence Alignment - Questionnaire

Part I: Basic information

Your name 

Part II: Sequence Alignment

A. Using the given parameters, calculate the local alignment score of the alignment below: 
Match reward = +1                 Mismatch penalty = -2
Gap opening penalty = -3       Gap extension penalty = -2
GAGAC--CTAGAAC
  |||  |||| ||
CTGACGGCTAGTAC
B. How comfortable are you in calculating alignment scores?
C. How comfortable are you in filling out a scoring table?

D. Do you understand the notion of word-searching as done by Blast? 

E. Do you see the mechanism by which Blast is able to run much faster than the Smith-Waterman algorithm? 

F. Do you understand how filtering the query sequence can alter the matches that are found?

G. Do you have an explanation for the mystery outlined in the Scenario? 

H. Comments/requests on this section?

Part III: BlastN
A. Were you able to download BlastN and get it to run on the accompanying test files? 

B. Were you able to get BlastN and to run on the files related to the scenario? 

C. (If you ran BlastN successfully) Do you understand why you got the results you did? 

D. Comments/requests on this section?


Part IV. Miscellaneous

A. Comments, concerns, questions?


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