Homework Assignments
1) Select a protein from OMIM concerning the disease of interest to you.2) Search your protein for motifs with the MyHits Motif Scan Query. Be sure to Include Protsite Patterns, Prosite Frequent Patterns, Prosite Profiles, Prefiles, Pfam HMMSs (local Models) in your search. Please send me the MyHits you think are biologically significant and at least 1 or 2 hits which you think are not statistically or biologicially significant. Please note that only the Profiles have expectation values. The Patterns do not have a measure of statistical significance
3) Search your protein for blocks using the InterPro. Please send me a few of the InterPro domains hits you think are significant and at least 1 or 2 hits which you think are not statistically or biologically significant. Please note that the default graphic output of InterPro does not list expectation values. You must switch to the Tabular view to obtain the statistical significance.
4) Search your protein for homology using the BLAST method. Please report two or three hits which are both statistically and biologically significant. Also report two or three hits which you think are neither statistically nor biologically significant. If your protein family is very large, you may have to ask BLAST to return more hits to find statistically insignificant hits.
SwissProt Protein Sequence database
National Center for Biotechnology Information
