VCU Bioinformatics and Bioengineering Summer Institute
Computational Search for Gene Sequences - Questionnaire
(please press SUBMIT button when finished)

Part I: Basic information

Your name 

Part II: Old business - The Scenario

A. How comfortable are you with the function of Ogr and why it is worth our attention?"
B. How clear are you regarding the connection between Ogr and NucC?
C. Gail told us that most blast hits using Ogr as the query were to prophages. Do you have a good idea what this means?
D. Gail told us that some hits were NOT to prophages, in particular one hit in the S. marcescens genome. Do you have a good idea why she thought this interesting?
E. Do you understand why Gail was surprised not to find a hit in the S. marcescens genome when she blasted with NucC protein?

F. Do you have an explanation for why she didn't get the hit, i.e. the mystery outlined in the tour? 

G. How far did you get in the tour? Please indicate any steps in the tour you'd like us to go over

H. Comments regarding the biology and the scenario:

Part III: DNA 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?
H. Please choose up to four study questions that you would most like discussed in class:

SQ1 SQ2 SQ3 SQ4 SQ5 SQ6 SQ7SQ8
I. Comments for questions III.A through III.G:
Part IV: Miscellaneous
Put here anycomments, questions, suggestions, concerns you may have.

Thanks!

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