Introduction to Bioinformatics (Fall 2003)
Questionnaire on notes: Construction of programs to detect anomalous genes
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I. Basic Information

A. Your name 
II. Modification of Hamlet.pl
A. Have you succeeded in incorporating FastA_module into Hamlet? 

B. How far are you along in modifying Hamlet.pl (henceforth called MakeMarkov.pl) so that it accesses individual genes of the training set? 

C. How far are you along in modifying MakeMarkov.pl so that it can analyze DNA sequences? 

D. How comfortable are you in understanding the model produced by MakeMarkov.pl, using 6803PHX.nt as the training set (and using Display_hash.pl to show you the contents of the model)? 
 
Comments for questions II.A through II.D:

III. Miscellaneous
A. How ready do you feel to go on to the last step of this project: using the Markov model produced by MakeMarkov to analyze all genes within a genome to detect putative alien genes? 

B. Please choose study questions from the notes that you would most like discussed in class:

SQ1 SQ2 SQ3 SQ4 SQ5 SQ6 SQ7
C. Put here any miscellaneous comments, questions, suggestions, concerns you may have.
 

Thanks!

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