BNFO 301 
Introduction to Bioinformatics
Questionnaire on: Finding Regulatory Motifs
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(If you encounter a question you've answered in a previous questionnaire and nothing has changed, just skip over it)
Spring 2015 


I. Basic Information

A. Your name 
II. Old Business
  1. Any parting concerns about Search for FMRP?

     
  2. Any parting concerns about Problem Set 5?

     
  3. Any parting concerns about phage biology, as discussed in the first couple of pages of Gene Regulation and Bacteriophages?
    • Do you understand what lysogeny is and why it might serve the bacteriophage?
    • Do you understand the need for a general repressor in lysogenic phage?
    • Anything other phage-related issues?
III. Gene Regulatory Sequences (how protein-binding sites work)
  1. Do you understand the different levels of gene regulation?
  2. Do you understand the relationship between transcriptional proteins (like RNA polymerase and repressors) and specific DNA sequences?
  3. Can you recognize sequences to which lambda repressor binds?
  4. Do you understand the power of regulatory feedback loops?
  5. DO you understand how the interplay between the lambda repressor and Cro protein might achieve a stable decision of lysogeny vs lysis?
  6. Anything other regulation-related issues?
  7. Any study questions that could use some discussion amongst SQ6-SQ21?
     
IV. Finding Regulatory Motifs
  1. How far did you get in the tour Search for Regulatory Sequences?

     
  2. Do you understand the different search methods (exact match, pattern match, COUNTS-OF-K-MERS) and why they give different results?
  3. Do you understand how MOTIFS-IN works and how its related to PSSMs?
  4. Do you understand the output of MOTIFS-IN?
  5. Were you able to find the lambda operators using MOTIFS-IN?
  6. Were you able to find the regulatory sequences of interset to Gomathi et al (2007)?
     

Do you have any favorite study questions (SQ1-SQ22) you think need discussion?  

V. Problem Set 6 (Statistics)
Any issues regarding Problem Set 5?
VI. Miscellaneous
Any other comments, questions, suggestions, or concerns you may have?
Any concerns about the research project?

Thanks!

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