Quiz: Jan 28, 2015

Create a page on the wiki called cgss15:students:bradpitt:quiz:2015-01-28, where you replace bradpitt with your actual Wiki username. Use this page to provide your answers for the following questions.

  1. Exact matches are easier and much quicker to compute than approximate matches. Why do read mapping software packages then implement approximate matching?
  2. In the context of read mapping, what is the difference between local alignment and (semi-)global alignment? Under what conditions would a local alignment be preferable?
  3. It is common for some reads to map to multiple locations in the genome or transcriptome. In some cases, a single mapping is clearly better than the alternatives (as measured by the scored alignment). In many cases though, there are 2 or more locations to which the read maps with similar scores.
    1. What are some potential causes of this behavior?
    2. What are some potential issues with reporting a large number of alignments for individual reads?
  4. What is the limitation to using software like BLAST to map short reads? What is the limitation to using a spliced alignment algorithm like GeneSeqer?
cgss15/quiz/2015-01-28.txt · Last modified: 2015/01/28 10:10 by standage
 
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