BNFO 301 
Introduction to Bioinformatics
Questionnaire on Genome Analysis Tour of Gomathi et al (2007)
(please press SUBMIT button when finished)
(and please don't use quotation marks in your answers. They break the questionnaire program!)
Spring 2011 

I. Basic Information

A. Your name 
II. Tour of Hatfull et al (2008) (old business)

  • Any issues remaining with this article? For instance...
  • Are you comfortable with dotplots, such as the one shown in Fig. 2?
  • Are you comfortable constructing families of proteins such as those shown in Fig. 3 (I mean doing it yourself)?
  • Are you comfortable with the meaning and significance of apparent mosaicism, as illustrated in Fig. 4?
  • Any other questions on your mind about the article or related matters?
     
III. Tour of Gomathi et al (2007)

  • How far did you get?
  • Do you understand how temperate phages differ from virulent phages and how you might identify a temperate phage from an analysis of its genome?
  • Do you understand how to use GeneMark to identify open reading frames (as well as its limitations)?
  • Do you understand how to look for transmembrane regions in proteins and why this might be something of interest?
  • Do you understand how to (in some cases) identify the family of a protein? ...and what a protein family is?
  • Do you understand how you might identify repeated sequences in a phage genome and why that might be of interest?
  • Ideas on how to identify an attachment site of an unknown temperate mycobacteriophage?
     
IV. Miscellaneous

  • Have you made initial contact with members of your research group?
  • Other miscellaneous comments, questions, suggestions, concerns?
     

Thanks!

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