BNFO 301
Introduction to Bioinformatics
Questionnaire on: Finding DNA Regulatory Sequences
(please press SUBMIT button when finished)
Spring 2005

I. Basic Information

A. Your name 
II. DNA Regulatory Sequences
A. How comfortable are you with the broad mechanism by which DNA binding protein may regulate gene expression? 

B. How comfortable are you with interpretting the alignment shown in Fig. 3? 

C. The sequences of the first three organisms listed in Fig. 3 are in BioLingua. Would you be able to extract the sequences shown on your own?

D. Do you understand the problem of using consensus patterns to find unknown regulatory sequences?

Comments re
regulatory DNA

III. Position-specific scoring matrices

A. How comfortable are you in calculating a Table of occurrences (Table I.B), given a set of aligned sequences? 

B. How comfortable are you in calculating a PSSM (Table I.C), given a set of aligned sequences? 

C. How comfortable are you in using a PSSM to score a given sequence (Table II)? 

D. Do you see the potential use of Meme?

Comments re
PSSMs

IV. Miscellaneous
A. Do you have a clue on how to proceed with your Project Proposal? With your project?

B. How are things going?

Thanks!

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