ApiDB/EuPathDB Workshop

Population data Exercises

Brian Brunk
Tuesday, June 10th - 10:45 am

Exercise 1: Isolates

  1. How many isolate records are there?
  2. How did you figure it out?
  3. What, in your opinion, is the most interesting isolation source?

Exercise 2 : SNPs

  1. Find all SNPs in the falciparum DHFR gene that would make good genetic markers (i.e., have at least two strains represented for each allele).
  2. How would you find good genetic markers distributed say every megabase along the falciparum genome?

Exercise 3 : Diversifying selection

  1. Find the falciparum genes that are the most diverse among sequenced strains and thus appear to be under diversifying selection.
  2. What strikes you about the known genes in this result set?

Exercise 4 : Drug Target Identification

  1. Try to identify your own set of the ten most promising drug targets! (hint: There are many ways to do this depending on your own assumptions and experience but one way would be to find genes that appear likely to be enymes, are conserved among Plasmodium species but not in humans, are expressed in merozoites and are under purifying selection (i.e., are not changing rapidly)).