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Aligning Sequences With T-Coffee

Aligning Sequences With T-Coffee. Cédric Notredame Comparative Bioinformatics Group Bioinformatics and Genomics Program. T-Coffee and Concistency…. SeqA GARFIELD THE LAST FAT CAT. SeqB GARFIELD THE FAST CAT. SeqC GARFIELD THE VERY FAST CAT. SeqD THE FAT CAT.

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Aligning Sequences With T-Coffee

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  1. Aligning SequencesWithT-Coffee Cédric Notredame Comparative Bioinformatics Group Bioinformatics and Genomics Program

  2. T-Coffee and Concistency… SeqA GARFIELD THE LAST FAT CAT SeqB GARFIELD THE FAST CAT SeqC GARFIELD THE VERY FAST CAT SeqD THE FAT CAT SeqA GARFIELD THE LAST FA-T CAT SeqB GARFIELD THE FAST CA-T --- SeqC GARFIELDTHEVERY FAST CAT SeqD -------- THE ---- FA-T CAT

  3. X Y Consistency: Conflicts and Information X Y W Z + X Z + Non Consistent OR Consistent Y Y W Z W Z Y OR Y X X X W Z W Z

  4. T-Coffee and Concistency… SeqA GARFIELD THE LAST FAT CAT Prim. Weight =88 SeqB GARFIELD THE FAST CAT --- SeqA GARFIELD THE LAST FA-T CAT Prim. Weight =77 SeqC GARFIELDTHE VERY FAST CAT SeqA GARFIELD THE LAST FAT CAT Prim. Weight =100 SeqD -------- THE ---- FAT CAT SeqB GARFIELD THE ---- FAST CATPrim. Weight =100 SeqC GARFIELDTHEVERY FAST CAT SeqC GARFIELDTHEVERY FAST CAT Prim. Weight =100 SeqD -------- THE ---- FA-T CAT

  5. SeqA GARFIELD THE LAST FAT CAT Prim. Weight =88 SeqB GARFIELD THE FAST CAT --- SeqA GARFIELD THE LAST FA-T CAT Prim. Weight =77 SeqC GARFIELDTHE VERY FAST CAT SeqA GARFIELD THE LAST FAT CAT Prim. Weight =100 SeqD -------- THE ---- FAT CAT SeqB GARFIELD THE ---- FAST CATPrim. Weight =100 SeqC GARFIELDTHEVERY FAST CAT SeqC GARFIELDTHEVERY FAST CAT Prim. Weight =100 SeqD -------- THE ---- FA-T CAT SeqA GARFIELD THE LAST FAT CAT Weight =88 SeqB GARFIELD THE FAST CAT --- SeqA GARFIELD THE LAST FA-T CAT Weight =77 SeqC GARFIELDTHE VERY FAST CAT SeqB GARFIELD THE ---- FAST CAT SeqA GARFIELD THE LAST FA-T CAT Weight =100 SeqD -------- THE ---- FA-T CAT SeqB GARFIELD THE ---- FAST CAT T-Coffee and Concistency…

  6. SeqA GARFIELD THE LAST FAT CAT Weight =88 SeqB GARFIELD THE FAST CAT --- SeqA GARFIELD THE LAST FA-T CAT Weight =77 SeqC GARFIELDTHE VERY FAST CAT SeqB GARFIELD THE ---- FAST CAT SeqA GARFIELD THE LAST FA-T CAT Weight =100 SeqD -------- THE ---- FA-T CAT SeqB GARFIELD THE ---- FAST CAT T-Coffee and Concistency…

  7. T-Coffee and Concistency…

  8. T-Coffee and Concistency…

  9. T-Coffee and Concistency…

  10. Methods Scalability Data

  11. Running T-Coffee over the Web

  12. Available Servers and Flavors

  13. Which MSA Method ???

  14. Combining Many MSAs into ONE ClustalW MAFFT T-Coffee MUSCLE ???????

  15. Consistency and Accuracy

  16. What To Do Without Structures

  17. Using the M-Coffee Server

  18. Using the M-Coffee Server

  19. Integrating New Types of DataTemplate Based Sequence Alignments

  20. Templates Templates Template Aligner TARGET TARGET TARGET Experimental Data … Experimental Data … Template Alignment Template-Sequence Alignment Template based Alignment of the Sequences Primary Library

  21. Exploring The Template World

  22. Exploring The Template World

  23. 3D-Coffee/ExpressoIncorporating Structural Information

  24. Expresso: Finding the Right Structure Sources BLAST BLAST SAP Templates Templates Template Alignment Source Template Alignment Library Remove Templates

  25. PSI-CoffeeHomology Extension

  26. Exploring The Template World

  27. What is Homology Extension ? -Simple scoring schemes result in alignment ambiguities L ? L L

  28. What is Homology Extension ? L L Profile 1 L L L L L L L L L L L I L Profile 2 V L I L L L

  29. What is Homology Extension ? L L Profile 1 L L L L L L L L L L L I L V L Profile 2 I L L L

  30. PSI-Coffee: Homology Extension Sources BLAST BLAST Profile Aligner Templates Templates Template Alignment Source Template Alignment Library Remove Templates

  31. Benchmarks

  32. Do Benchmarks All Tell the same story? Based on

  33. Score: fraction of correct columns when compared with a structure based reference (BB11 of BaliBase).

  34. Consistency Score: fraction of correct columns when compared with a structure based reference (BB11 of BaliBase).

  35. Homology Extension Score: fraction of correct columns when compared with a structure based reference (BB11 of BaliBase).

  36. Structural Extension Score: fraction of correct columns when compared with a structure based reference (BB11 of BaliBase).

  37. T-Coffee and The World -Some Templates are obtained with a BLAST -Queries can be sent to the EBI or the NCBI -No Need for a Local BLAST installation BLAST/ SOAP Users sequences

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