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Visualise conservation

Visualise conservation. 1. Colour -> BLOSUM62. EMBO Workshop, Cape Town, 2014. Reduce redundancy. 1. Edit-> Remove Redundancy. 2. PICK “80%”. EMBO Workshop, Cape Town, 2014. 1. Edit-> Remove Empty Columns. EMBO Workshop, Cape Town, 2014. Define boundaries.

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Visualise conservation

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  1. Visualise conservation 1. Colour -> BLOSUM62 EMBO Workshop, Cape Town, 2014

  2. Reduce redundancy 1. Edit-> Remove Redundancy 2. PICK “80%”

  3. EMBO Workshop, Cape Town, 2014

  4. 1. Edit-> Remove Empty Columns EMBO Workshop, Cape Town, 2014

  5. Define boundaries EMBO Workshop, Cape Town, 2014

  6. Define boundaries 1. Colour -> Hydrophobicity EMBO Workshop, Cape Town, 2014

  7. EEVTES ER 2KX7 model 1 TUM, January 2013

  8. Trim alignment 1. CLICK on residue number bar to select column 2. Edit -> Remove right EMBO Workshop, Cape Town, 2014

  9. Trim alignment 1. CLICK on residue number bar to select column 2. Edit -> Remove left EMBO Workshop, Cape Town, 2014

  10. Save SEED alignment 1. File -> Save as “RcsD-ABL-SEED-ali.fasta” EMBO Workshop, Cape Town, 2014

  11. Create HMM and run against database(s) 1. CLICK on Start EMBO Workshop, Cape Town, 2014

  12. Create HMM and run against database(s) 1. CLICK on Choose File 2. Choose RcsD-ABL-SEED-ali.fasta EMBO Workshop, Cape Town, 2014

  13. First run against RP75 to see if anything has changed 1. CLICK on rp75 EMBO Workshop, Cape Town, 2014

  14. First run against RP75 to see if anything has changed NOW BEFORE

  15. Now we run against UniProtKB EMBO Workshop, Cape Town, 2014

  16. Check Scores EMBO Workshop, Cape Town, 2014

  17. Check Low Scores EMBO Workshop, Cape Town, 2014

  18. Define significance threshold EMBO Workshop, Cape Town, 2014

  19. Check taxonomic distribution EMBO Workshop, Cape Town, 2014

  20. Check taxonomic distribution EMBO Workshop, Cape Town, 2014

  21. Check architectures

  22. Save HMM EMBO Workshop, Cape Town, 2014

  23. Job done? EMBO Workshop, Cape Town, 2014

  24. Pick a target region 2KX7 TUM, January 2013 Schmöe et al. Structure 2011 EMBO Workshop, Cape Town, 2014

  25. Pick a target region RcsD_ABL (PF16359) 2KX7 TUM, January 2013 Schmöe et al. Structure 2011 EMBO Workshop, Cape Town, 2014

  26. Pick a target region RcsD_ABL (PF16359) 2KX7 TUM, January 2013 Schmöe et al. Structure 2011 EMBO Workshop, Cape Town, 2014

  27. Job done? 2KX7 2AYY Schmöe et al. Structure 2011 EMBO Workshop, Cape Town, 2014

  28. Job done? EMBO Workshop, Cape Town, 2014

  29. Exercise Run the UNIPROT ID: Q820A8 with the hmmer website (2 iterations) and observe results EMBO Workshop, Cape Town, 2014

  30. Exercise Run the UNIPROT ID: Q820A8 with the hmmer website (2 iterations) and observe results Run the Q820A8-PASTA-domain.fasta with the hmmer website (2 iterations) and observe results EMBO Workshop, Cape Town, 2014

  31. Exercise Run the UNIPROT ID: Q820A8 with the hmmer website (2 iterations) and observe results Run the this portion of the Q820A8 sequence VTLSDYSGISYDNAVSRLIALGIPESQIKRVDEESDKVEKDTVISQEPASGTAVDPKNDTITLHVSK with the hmmer website (2 iterations) and observe results EMBO Workshop, Cape Town, 2014

  32. Acknowledgements Rob Finn (Protein Family Team Leader) The Pfam Team: Penny Coggill Ruth Eberhardt JainaMistry John Tate IliasLavidas Alex Bateman (Protein sequence resources cluster) Sean Eddy -> HMMER3 (Janelia Farm) Erik Sonnhammer (Stockholm University) All organisers of the EMBO course, trainers and trainees EMBO Workshop, Cape Town, 2014

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