1. Applications Using standard Bioinformatics applications

2. Introduction

3. The overall plan for the regeneration of high quality annotation information as contained in the EMBL disk-file ISTN501 figWHAT.eps

4. Scientific Background To Mer Operon ● Function ● Genetic Structure and Regulation ● Mobility Of The Mer Operon

5. The principal proteins and their functions figPRINCIPLE.eps

6. Downloading The Raw DNA Sequence

7. Initial BLAST Sequence Similarity Search

8. Maxim 18.1 With BLAST scores, up is down and lower is better

9. http://opal.biology.gatech.edu/GeneMark/ GeneMark

10. The web-based interface to GeneMark as running at EBI figEBIGENEBANK.eps

11. Using BLAST to identify specific sequences

12. Dealing with false negatives and missing proteins

13. Over predicted genes and false positives

14. http://www.expasy.org/swissmod/ Structural Prediction With SWISS-MODEL

15. Maxim 18.2 The major limitation of ``homology modelling'' is that homology to a known structure is needed

16. Alternatives to homology modelling

17. Modelling with SWISS-MODEL

18. The SWISS-MODEL predicted structure of ORF2/MerP figORF2MERP.eps

19. The SWISS-MODEL predicted structure of ORF2/MerP, second version figORF2MERP2.eps

20. The SWISS-MODEL predicted structure of ORF3/MerA (A) figORF3MERAA.eps

21. The SWISS-MODEL predicted structure of ORF3/MerAB figORF3MERAB.eps

22. The SWISS-MODEL predicted structure of ORF6/TNR5 figORF6TNR5.eps

23. DeepView as a Structural Alignment Tool

24. The ORF2 and ORF3_A structures loaded into DeepView prior to structural alignment figDEEPVIEW.eps

25. DeepView's Iterative Magic Fit dialogue box figDEEPVIEWDIALOG.eps

26. Structural Alignment created using the DeepView's Iterative Magic Fit facility figDEEPVIEWEXAMPLE.eps

27. Selecting the current ``layer'' in DeepView figDEEPLAYER.eps

28. Possible Explanation Behind MerA/HMA Duplication Event figPOSSIBLE.eps

29. The structural alignment of ORF3_B and the ``official'' Mercury Reductase X-ray structure figCYSTEINES.eps

30. Maxim 18.3 Homology modelling can only model protein sequences similar to those which are already known

31. PROSITE and Sequence Motifs

32. Maxim 18.4 Searching large datasets with non-specific, short sequence fragments results in many false positives

33. http://www.expasy.org/prosite/ http://www.ebi.ac.uk/interpro/ http://www.geneontology.org ● http://www.kegg.org Using PROSITE patterns and matrices

34. Phylogenetics

35. A look at the HMA domain of MerA and MerP ------------------------------- SWISS-PROT IDs of MerP Proteins SWISS-PROT IDs of MerA Proteins ------------------------------- MERP_ACICA MERA_ACICA MERP_ALCSP MERA_ALCSP MERP_PSEAE MERA_BACSR MERP_PSEFL MERA_ENTAG MERP_SALTI MERA_PSEAE MERP_SERMA MERA_PSEFL MERP_SHEPU MERA_SERMA MERP_SHIFL MERA_SHEPU MERA_SHIFL MERA_STAEP MERA_STRLI MERA_THIFE -------------------------------

36. The multiple sequence alignment of the example proteins figLISTMERAMERP.eps

37. The EBI's tree graphical display figTREE.eps

38. Maxim 18.5 Whenever you make a statement, call for more research (money)!

39. Maxim 18.6 Database annotation is hard to do well, so be prepared to update it on a regular basis

40. Maxim 18.7 Automation can be very helpful when creating annotation, but to achieve the highest quality, humans are needed to make some value judgments

41. Maxim 18.8 Conclusions are based on the available data which, in this case, is the database annotation (which may or may not be current)

42. Where To From Here?