I. Basic Information

A. Your name 

A. How comfortable are you with the broad mechanism by which DNA binding protein may regulate gene expression? SelectVery much soModeratelySomewhat comfortableNot at all

B. How comfortable are you with interpretting the alignment shown in Fig. 3? SelectVery much soModeratelySomewhat comfortableNot at all

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? SelectCertainlyHave a plausible ideaSome vague ideasNot at all

D. Do you understand the problem of using consensus patterns to find unknown regulatory sequences? SelectCertainlyHave a plausible ideaSome vague ideasNot at all

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? SelectVery much soModeratelySomewhat comfortableNot at all

B. How comfortable are you in calculating a PSSM (Table I.C), given a set of aligned sequences? SelectVery much soModeratelySomewhat comfortableNot at all

C. How comfortable are you in using a PSSM to score a given sequence (Table II)? SelectVery much soModeratelySomewhat comfortableNot at all

D. Do you see the potential use of Meme? SelectCertainlyHave a plausible ideaSome vague ideasNot at all

Comments re PSSMs

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

B. How are things going?