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| 8. Protein motif identification |
Introduction Secondary databases gather information about protein domains and families in the form of regular expressions, fingerprints and profiles. Likewise they enable by means of appropriate tools to compare arbitrary protein sequence with sequences in database and so predict structure and function of this protein. - Database PROSITE – tool PrositeSearch
- Database Prints – tool PScan
- Database Pfam – tool HmmPfam
Task no. 1 Analyse protein sequence using programs BLAST, PrositeSearch, Pscan and HmmPfam. Then try to: - compare results of individual analysis. Are they equal? What a protein does it matter in your case?
- compare sensitivity of used algorithms
- compare, how do results of PrositeSearch differ, if search of patterns with high probablity of occurence is excluded and isn't excluded.
- find out, whether complete fingerprint was detected
- compare E values from BLAST and HmmPfam. Are they equal? If not, try to explain why.
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