Exercise 3

In your groups search your sequence from the previous exercise against the Rfam database.

• What is the species distributions and possible function for the homologues of your sequence?
• What is the function of your sequence?
• Is it related to any other type of RNA family?
• For the brave students:
  • Download the seed alignment for the family.
  • Examine the alignment using Ralee, can you improve it?
  • Build a HMMER profile HMM and scan it against the example genome below. See the HOWTO for more information.
    • WARNING: this exercise has not been completely debugged yet.
  • Build an INFERNAL CM and scan it against the example genome below. See the HOWTO for more information.