Introduction to Bioinformatics (Fall 2003)
Questionnaire on notes: Progress, Scoring, Protein alignment
(please press SUBMIT button when finished)

I. Basic Information

A. Your name 
II. Progress in Scenario 3
We didn't get as far as one might have hoped in Wednesday's notes, but maybe you were able to progress on your own, so I feel the need to ask some questions again:
A. How comfortable are you now in your understanding of two-dimensional arrays, at least to the extent of being able to access elements within them? 

B. Have you now gotten homegrown BlastN to run? 

C. Have you now implemented a subroutine that prints out a scoring table somewhere within BlastN? 

D. What progress have you made in understanding the differences between homegrown BlastN and NCBI's Blast-2-Sequences, by making changes in the adjustable parameters of the programs? 

 
Comments for questions II.A through II.D:
III. Evaluating significance of scores
A. How comfortable are you with the explanation behind equation 1 in the notes, i.e. how to calculate the expected number of exact matches between two sequences? 
B. Can you find in Blast output (from the web) the E-value, raw score, and bits score? 

C. How comfortable are you with the relationship between these three quantities? 

 
Comments for questions III.A through II.C:
IV. Protein alignments
A. How comfortable are you with reading a PAM frequency table (e.g. Table 2) and a log odds table (e.g. Fig. 3)? 
B. How comfortable are you with the distinctions between the different versions of PAM and between the different versions of BLOSUM? 

C. How comfortable are you calculating the score of an amino acid alignment? 

 
Comments for questions IV.A through II.C:
V. Design your class
A. Please choose up to four study questions that you would most like discussed in class:
SQ1 SQ2 SQ3 SQ4 SQ5 SQ6 SQ7 SQ8 SQ9 SQ10
B. Do you think it more profitable to pause to spend time in class on fooling around with BlastN, or would you prefer that we spend that time understanding the theory behind protein alignments and scoring? (respond below)
C. Put here any miscellaneous comments, questions, suggestions, concerns you may have. Tell us what you need.
 

Thanks!

REMEMBER TO CLICK SUBMIT! (or click RESET to start over)