Introduction to Bioinformatics (Fall 2003)
Questionnaire on notes: Parsing programs
(please press SUBMIT button when finished)

I. Basic Information and Miscellaneous

A. Your name 
II. Mechanics
A. Were you able to download and install Blast successfully to your own computer? 

B. Were you able to download the set of proteins from E. coli K-12 and from one of the two pathogenic E. coli to your own computer? 

C. Were you able to run FormatDB to create a database of proteins from E. coli K-12? 

D. Were you able to run BlastAll to compare the set of proteins of the pathogenic strain against the database of K-12 protein, producing a file with a size of about 40 megabytes? 

E. Were you able to examine a portion of the output of the program ? 

 
Comments for questions II.A through II.E:
III. Parsing the output from Blast
A. Do you know where to find each of the seven items listed in the notes (e.g. Query name) in the output from Blast? 

B. Do you know where each of the seven items in the output of BlastParser comes from? 

C. Were you able to modify and run BlastParser so that it opened the file you created with BlastAll? (If you couldn't, make sure that you downloaded BlastParser into the same directory as the output from Blast, presumably /Blast, and that you are in that directory when you try to run the program) 

D. Please choose up to three study questions that you would most like discussed in class:

SQ1 SQ2 SQ3 SQ4 SQ5
Comments for questions III.A through II.C:
IV. Regular expressions, capturing matched patterns
A. How comfortable are you with interpretting and using character classes in regular expressions, to the extent that they are used in Blast Parser? Example:
    my ($query, $query_description) = /^Query=\s+(\w+)\W+(.+)/;

B. How comfortable are you with interpretting and using repetition symbols in regular expressions, to the extent that they are used in Blast Parser? Example:
    my ($query, $query_description) = /^Query=\s+(\w+)\W+(.+)/;

C. How comfortable are you with interpretting and using expressions that capture matched patterns, to the extent that they are used in Blast Parser? Examples:
     my ($query, $query_description) = /^Query=\s+(\w+)\W+(.+)/;
  $subject_description = $3;

D. Please choose up to three study questions that you would most like discussed in class:

SQ6 SQ7 SQ8 SQ9 SQ10 SQ11
 
Comments for questions IV.A and IV.D:
V. Miscellaneous
A. Put here any miscellaneous comments, questions, suggestions, concerns you may have. E.g., Need 1-to-1 help with Perl? Wondering why we need Perl at all? Aaaargggh?
 

Thanks!

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