Profile/HMM Homework
October 30, 2008 Doug Brutlag Homework Assignment Number 7
For this homework assignment take between 10 and 15 protein sequences from a single protein family and that are at least 30% identical and:
1) make an HMM with them using the Decypher computer. The esiest way to do this is to use a single sequence as a query in a Smith Waterman or BLAST database search of Swiss-Prot and then to chose 10-15 sequences from the list of similar sequences that are 30% identical or better.2) use the HMM to search the Swiss-Prot database for additional members of the familiy
3) take one member of your protein family and perform a two or three iteration PSI-BLAST search of Swiss-Prot.
4) take the same member of your protein family and perform a standard BLAST search of Swiss-Prot.
Describe the resulting searches in a message to homework218@cmgm.stanford.edu. Mention how many of your initial proteins are in the statistically significant range in each search. Ask how many of the statistically significant hits are biologically relevant (either by means of functional similarity or strutural similarity). Are there more statistically significant sequences in the BLAST search, the HMM search or in the PSI-BLAST search.
This assignment is due on December 5, 2008. If you have not yet sent me a final project proposal, please do so immediately.