BNFO 301 
Introduction to Bioinformatics
Questionnaire on: Computational detection of origins of replication
(please press SUBMIT button when finished)
(If you encounter a question you've answered in a previous questionnaire and nothing has changed, just skip over it)
Spring 2014 


I. Basic Information

A. Your name 
II. Old Business
A. Any final thoughts on Problem Set 1?
   

B. Anything worth discussing about increasing your abilities in BioBIKE?
   

C. Any final thoughts on Fuller et al (1984)?
   

D. Any final thoughts on the presentation of probability tools?
   

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?

   

Choose up to six questions from these notes that you would most like discussed in class:

SQ1  SQ2  SQ3  SQ4  SQ5  SQ6  SQ7  SQ8  SQ9 
SQ10  SQ11  SQ12  SQ13  SQ14  SQ15  SQ16  SQ17 
SQ18  SQ19  SQ20 SQ21  SQ22  SQ23  SQ24  SQ25 
SQ26  SQ27  SQ28  SQ29  SQ30
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?

   

Choose up to five questions from these notes that you would most like discussed in class:

SQ1  SQ2  SQ3  SQ4  SQ5  SQ6  x SQ7  SQ8  SQ9 
SQ10  SQ11  SQ12  SQ13  SQ14  SQ15  SQ16  SQ17 
SQ18  SQ19  SQ20 SQ21  SQ22  SQ23  SQ24  SQ25 
SQ26  SQ27 
V. Miscellaneous
Any other comments, questions, suggestions, or concerns you may have?

Thanks!

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