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Exercises

Exercises. Pairwise alignment Homology search (BLAST) Multiple alignment (CLUSTAL W) Iterative Profile Search: Profile Search Pfam Prosite PSI-BLAST SAM. Overview. Query Sequence Unknown. Blast. Blast Sequence to search for close homologs. ClustalW. PFAM PROSITE.

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Exercises

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  1. Exercises • Pairwise alignment • Homology search (BLAST) • Multiple alignment (CLUSTAL W) • Iterative Profile Search: • Profile Search • Pfam • Prosite • PSI-BLAST • SAM

  2. Overview Query Sequence Unknown Blast Blast Sequence to search for close homologs ClustalW PFAM PROSITE Make a multiple sequence alignment Search pFAM, Prosite for conserved motifs HMMer, PSSM PSI-blast Generate profile or HMM You detected homology with an annotated protein family Profile Search Search database for remote homologs

  3. Terminal Oxidases Cytc e- Fe Fe Fe OUT e- e- CuB Fe Fe IN • Unknown protein is a heme cupper oxidase • Enzyme that reduces O2 to H2O in respiratory chain O2 I H2O • Subunit contains 2 hemes and a Cu prosthetic group • The residues that are ligands of these groups have been conserved in all types of terminal oxidase complexes

  4. Terminal Oxidases O2 cytbc1 ? Cytc H2O NADH Nadh.dh e- cytochrome c oxidase e- e- quinol O2 succinate succ.dh ? H2O e- quinol oxidase e- e- O2 H2O H+ H+

  5. Multiple Alignment

  6. Multiple Alignment Multiple alignment: standard gap cost Ligands Cu center Prosite pattern Ligands hemes

  7. Multiple Alignment Ligands Cu center Multiple alignment: large gap cost Prosite pattern Ligands hemes

  8. Phylogenetic Tree Tree based on subselection

  9. PROSITE

  10. Prosite

  11. Prosite

  12. Prosite

  13. Prosite

  14. Prosite

  15. Prosite

  16. Prosite Prosite domain

  17. Pattern & profile

  18. pFAM

  19. Pfam

  20. Pfam

  21. Pfam

  22. Pfam COX family

  23. Pfam

  24. Pfam

  25. Pfam

  26. Pfam

  27. Pfam

  28. Pfam

  29. BLOCKS

  30. Blocks

  31. Overview Query Sequence Unknown Blast Blast Sequence to search for close homologs PFAM PROSITE Make a multiple sequence alignment Search pFAM, Prosite for conserved motifs HMMer, PSSM PSI-blast Generate profile or HMM You detected homology with an annotated protein family Profile Search Search database for remote homologs

  32. PSI-BLAST

  33. PSI-BLAST • PSI BLAST • Start from a single sequence • Blast it against NCBI • Select high scoring hits • Perform multiple alignment • Construct profile • Iterate and find remote homologs • Usually cut the sequence in pieces • Avoid to give as input multi domain proteins

  34. PSI-BLAST

  35. PSI-BLAST

  36. PSI-BLAST

  37. PSI-BLAST

  38. PSI-BLAST

  39. PSI-BLAST

  40. SAM

  41. SAM http://www.cse.ucsc.edu/research/compbio/HMM-apps/HMM-applications.html

  42. SAM

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