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Applications

Using standard Bioinformatics applications. Applications. Introduction. figWHAT.eps. The overall plan for the regeneration of high quality annotation information as contained in the EMBL disk-file ISTN501. Scientific Background To Mer Operon. Function Genetic Structure and Regulation

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Applications

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  1. Using standard Bioinformatics applications Applications

  2. Introduction

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

  4. Scientific Background ToMer Operon • Function • Genetic Structure and Regulation • Mobility Of The Mer Operon

  5. figPRINCIPLE.eps The principal proteins and their functions

  6. Downloading The Raw DNA Sequence

  7. Initial BLAST Sequence Similarity Search

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

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

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

  11. Using BLAST to identify specific sequences

  12. Dealing with false negatives and missing proteins

  13. Over predicted genes and false positives

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

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

  16. Alternatives to homology modelling

  17. Modelling with SWISS-MODEL

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

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

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

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

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

  23. DeepView as a Structural Alignment Tool

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

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

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

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

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

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

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

  31. PROSITE and Sequence Motifs

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

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

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

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

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

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

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

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

  42. Where To From Here?

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