Practical Project 2011-2012

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Class 1


Class 2


Intermediate Deliverable

In order to be able to give you feedback at a moment where you may still benefit from it, please hand in per group the following:

  • Answers to the questions in the practical manual
  • your code
  • At least one ROC plot and (preliminary) discussion on your results
  • a specification of the (planned) work division among the members of your group
    • you're free split the work whichever way you like -- everything joint, or everyone his/her separate chunk
    • but you need to understand (i.e., be able to explain - not reproduce) the contributions from all your groupmembers

Deadline for delivering this as a group to either me, Sanne, or Punto on Monday, October 10. We will give you feedback per e-mail later that week, on Tuesday October 13.


PSI-Blast

PSI-Blast is a much better homology detection algorithm than Blast is, particular for 'remote' homologs (larger sequence differences). So, we would like you to also test PSI-blast on your proteins. Unfortunately, there is no 'easy' way to call PSI-blast from within a script. So, if (and only if) you have spare time left in your group and there is someone in your group who knows how to do it (e.g. using BioPython), you may repeat the whole benchmarking process you did for Blast also with PSI-blast. This is a not required, optional bonus part.


Deadline

By popular demand: The deadline for delivering the report will be Friday October 21Monday October 24 by e-mail to one of us (Anton, Sanne, or Punto). This deadline is final - there simple isn't time left before the exam and presentations for further postponing.


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