VCU Bioinformatics and Bioengineering Summer Institute
Genes Determining Plant-Cyanobacterial Symbioses / Blast
(Please don't use quotation marks in your answers. They break the questionnaire program!)

Part I: Basic information

Your name 
 

Part II: Analysis of cDNA library

The primary purpose of our meeting last Thursday was to make clear some issues that need to be addressed in analyzing the sequences from a cDNA library. You can remind yourself of what they were by looking at the presentation under June 4 on the simulation's web page.
  • Are you comfortable with the procedure by which the library was constructed?
  • Are you comfortable with the procedure by which the sequences were assembled?
  • Do you see why it is important to look for stray adapter sequences?
  • Do you see why it is important to use Blast to find protein sequences similar to those that might be encoded by elements of the cDNA library?

Answers to these and possibly other related questions that may occur to you
     

 

Part III: The Mind of Blast

How far did you get in the notes entitled Blast: Alignment of pairs of sequences? 

A. Choose study questions that you would most like discussed in class:

SQ1  SQ2  SQ3  SQ4  SQ5  SQ6  SQ7  SQ8  SQ9  SQ10  SQ11  SQ12  SQ13 

B. How Blast works

  • Do you understand how Blast aligns DNA sequences?
  • Do you understand how the BLOSUM62 table is used in protein sequence alignments?
  • Do you understand why filtering is sometimes desirable?
  • Do you understand how word-based searches work and why they greatly speed up the process?
     

C. How Blast is interpreted

  • Do you understand intuitively the concept of an Expect score?
  • Do you understand how to interpret an E score?
  • Do you understand why it should vary depending on the database size?
     

D. Why does Blast fail?

  • (Mystery #1) Do you understand why BlastN failed to find a sequence matching the human hemoglobin gene but BlastX was successful?
  • (Mystery #2) Do you understand why BlastN failed to find a match to the PCR fragment even though the alignment looks by eye to be very good?
     
 

Part IV: Miscellaneous

  • Any remaining difficulties accessing your web site?
  • Progress on developing a research proposal?
  • Concerns about presenting your research proposal Tuesday night?
  • Integration into new lab proceeding?
  • Any other comments, questions, concerns?
     

Thanks!

REMEMBER TO CLICK SUBMIT! (or click RESET to start over)