Faction 2: Functional Annotation Lab Exercises

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Functional Annotation HW (Due March 31 at 11:59pm email answers to func.anno.f2@gmail.com)

Setup: Download TMHMM (http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm) Download PilerCR (http://www.drive5.com/pilercr/) Download SignalP (http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp)

If you download these tools to the server, please uninstall them after turning in your homework.

Question 1: PilerCR For question 1, use /data/home/ccolon6/hwFiles/test.fasta as your input fasta file.

  a)Run PilerCR with the test file.  How many CRISPRs did it find? (5 points)
  b)Post a screenshot of the results under Array 1 from the output file. (5 points)
  c)What is the function of CRISPRs? (5 points)

Question 2: SignalP For question 2, use /data/home/amo3/hw/protein.fasta

  a)Run SignalP with the test protein sequence file. Describe the meaning of the output. (5 points)
  b)Post a screenshot of the first few lines of the output. (5 points)
  c)Is the first input sequence a signal peptide? Explain how you know. (5 points) 

Question 3: TMHMM For question 4, use this genome:CP016504.1 from NCBI

  a)Run TMHMM with the test protein sequence file. Explain the output. How many TMHs were predicted? (5 points)
  b)Post the screenshot of first few lines of your output. (5 points)
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