BNFO 301 
Introduction to Bioinformatics
Questionnaire on: Computational detection of origins of replication
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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

A. Any parting thoughts on Problem Set 1?
   

B. Anything we might discuss that could increase your abilities in BioBIKE?
   

C. Any parting thoughts on Fuller et al (1984) (and its companion) (and the special discussion of restriction digestion)?
   

D. Any parting thoughts on the presentation of probability tools and the calculation of probability?

III. Computational detection of repeated sequences

A. How far have you gotten in these notes?
   

Your thoughts on the following issues?

B. Have you found in the E. coli genome (e.g. using BioBIKE) the sequence given by Fuller et al (1984)?

C. Do you understand how (in principle) to go about finding k-mer frequencies in texts or sequences?

D. Are you comfortable with the discussion on how many comparisons would be required to implement an algorithm?

E. Are you comfortable interpretting the results of the COUNTS-OF-K-MERS funtion, both with and without the BOTH-STRANDS option?

F. Were you able to find computationally all instances of the given DnaA-binding site in the origin region?

G. How comfortable are you in devising (not necessarily implementeing) an algorithm to find origins of replications in bacterial genomes?

   

H. Choose up to six study questions from these notes you would most like discussed in class and explain why.
     

IV. Calculation of probability of rare events

A. How far have you gotten in these notes?
   

Your thoughts on the following issues?

B. The remarkableness within the first 100 nucleotides of the genome of Prochlorococcus marinus Med4?

C. The calculation of the probability of encountering one TTTT in four specific nucleotides?

D. The calculation of the probability of encountering three TTTT's in a region of DNA?

E. The calculation of combinations and its relevance to bioinformatics?

F. Binomial coefficients and the Poisson expression to calculate probabilities?

G. Estimating probabilities by computer simulation?

   

H. Choose up to five study questions from these notes you would most like discussed in class and explain why.
     

V. Miscellaneous

Any other comments, questions, suggestions, or concerns you may have?

Thanks!

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