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!)
 
  This is a long questionnaire.
There is a large backlog of issues that have not yet been addressed.
Spring 2012 

I. Basic Information

A. Your name 
II. Search for FMRP in Drosophila

  • How far were you able to get in the Search for FMRP in Drosophila?
  • Do you feel comfortable finding genes and proteins in the NCBI database?
  • Do you have a basic idea what Blast is doing and how it works?
  • Do you have an idea why nucleotide blast failed to find the desired gene while the indirect route through protein blast worked?
  • Do have at least a faint inkling why the NCBI database and Blast might be useful in analyzing an unknown phage genome?
  • Any favorite study questions you want to discuss? What's the problem with them?
     
III. Tour of Hatfull et al (2008)

  • How far were you able to get in the tour (Part I and Part II)?
  • Do you appreciate the difference between a review article and a research article?
  • Are you comfortable with notions of orf and GC fraction? If not, what's the problem?
  • Are you comfortable with dotplots, such as the one shown in Fig. 2? If not, what's the problem?
  • Are you comfortable constructing families of proteins such as those shown in Fig. 3 (I mean doing it yourself)? If not, what's the problem?
  • Are you comfortable with the meaning and significance of Fig. 4? If not, what's the problem?
  • Any other specific issues on your mind about the article or related matters?
  • Favorite study questions? What's the problem with them?
     
IV. 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?
  • Favorite study questions? What's the problem with them?
     
V. Mapping and Looping

  • How far have you gotten in the notes Introduction to mapping, including (of course) EXPLORING the examples?
  • How far have you gotten in the notes Elements of a loop, including (as always) EXPLORING the examples?
  • Do you have a basic idea what mapping does? If not, what's the problem?
  • Do you have a basic idea what looping does? If not, what's the problem?
  • Do you have an idea why mapping and looping might be useful in analyzing an unknown phage genome? If not, what's the problem?
  • Anything specific that's not going as expected?
     
VI. Miscellaneous

  • Have you established good communication with members of your research group?
  • Other miscellaneous comments, questions, suggestions, concerns?
     

Thanks!

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