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 SeqA GARFIELD THE LAST FA-T CAT SeqB GARFIELD THE FAST CA-T --- SeqC GARFIELD THE VERY FAST CAT SeqD THE ---- FA-T CAT
Consistency: Conflicts and Information Y WZ X Z Y Z W Y Z X W X Y OR + + Non Consistent Consistent Y WZ Y Z W OR X X X
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 GARFIELD THE VERY FAST CAT SeqA GARFIELD THE LAST FAT CAT Prim. Weight =100 SeqD THE ---- FAT CAT SeqB GARFIELD THE ---- FAST CAT Prim. Weight =100 SeqC GARFIELD THE VERY FAST CAT SeqC GARFIELD THE VERY FAST CAT Prim. Weight =100 SeqD THE ---- FA-T CAT
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 GARFIELD THE VERY FAST CAT SeqA GARFIELD THE LAST FAT CAT Prim. Weight =100 SeqD THE ---- FAT CAT SeqB GARFIELD THE ---- FAST CAT Prim. Weight =100 SeqC GARFIELD THE VERY FAST CAT SeqC GARFIELD THE VERY 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 GARFIELD THE 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… SeqA GARFIELD THE LAST FAT CAT Weight =88 SeqB GARFIELD THE FAST CAT --- SeqA GARFIELD THE LAST FA-T CAT Weight =77 SeqC GARFIELD THE 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…
Methods Data Scalability
Running T-Coffee over the Web
Available Servers and Flavors
Which MSA Method ???
Combining Many MSAs into ONE MUSCLE MAFFT ClustalW ??????? T-Coffee
Consistency and Accuracy
What To Do Without Structures
Using the M-Coffee Server
Integrating New Types of Data Template Based Sequence Alignments
Experimental Data … TARGET Experimental Data … TARGET Template Aligner Template-Sequence Alignment Primary Library Template Alignment Template based Alignment of the Sequences Templates TARGET
Exploring The Template World TemplateGeneratorAlignment Method RNA StructurePredictionRNA Aligner Protein StructureBLAST vs PDB3D Aligner ProfileBLAST vs NRProfile/Profile Alignment Gene StructureENSEMBLGenome Aligner PromoterTransfacMeta-Aligner
Exploring The Template World TemplateGeneratorAlignment Method Mode RNA Structure PredictionRNA Aligner R-Coffee Protein Structure BLAST /PDB3D Aligner 3D-Coffee Profile BLAST/NRProfile/Profile PSI-Coffee Gene Structure ENSEMBLGenome Aligner Exoset Promoter TransfacMeta-Aligner Meta-Coffee
3D-Coffee/Expresso Incorporating Structural Information
Expresso: Finding the Right Structure Sources Templates Library BLAST SAP Template Alignment Source Template Alignment Remove Templates Templates
PSI-Coffee Homology Extension
Exploring The Template World
What is Homology Extension ? LL L ? -Simple scoring schemes result in alignment ambiguities
What is Homology Extension ? LL L L L L L L L L L I V I L L L L L L L Profile 1 Profile 2
What is Homology Extension ? LL L L L L L L L L L I V I L L L L L L L Profile 1 Profile 2
PSI-Coffee: Homology Extension Sources Templates Library BLAST Template Alignment Source Template Alignment Remove Templates Templates Profile Aligner
Benchmarks
Do Benchmarks All Tell the same story? Based on
Method TemplateScoreComment ClustalW-2ProgressiveNO22.74 PRANKGapNO26.18Science2008 MAFFTIterativeNO26.18 MuscleIterativeNO31.37 ProbConsConsistencyNO40.80 ProbConsMonoPhasicNO37.53 T-CoffeeConsistencyNO42.30 M-Coffe4ConsistencyNO43.60 PSI-CoffeeConsistencyProfile53.71 PROMALConsistencyProfile55.08 PROMAL-3DConsistencyPDB D-CoffeeConsistencyPDB61.00Expresso Score: fraction of correct columns when compared with a structure based reference (BB11 of BaliBase).
Method TemplateScoreComment ClustalW-2ProgressiveNO22.74 PRANKGapNO26.18Science2008 MAFFTIterativeNO26.18 MuscleIterativeNO31.37 ProbConsConsistencyNO40.80 ProbConsMonoPhasicNO37.53 T-CoffeeConsistencyNO42.30 M-Coffe4ConsistencyNO43.60 PSI-CoffeeConsistencyProfile53.71 PROMALConsistencyProfile55.08 PROMAL-3DConsistencyPDB D-CoffeeConsistencyPDB61.00Expresso Score: fraction of correct columns when compared with a structure based reference (BB11 of BaliBase). Consistency
Method TemplateScoreComment ClustalW-2ProgressiveNO22.74 PRANKGapNO26.18Science2008 MAFFTIterativeNO26.18 MuscleIterativeNO31.37 ProbConsConsistencyNO40.80 ProbConsMonoPhasicNO37.53 T-CoffeeConsistencyNO42.30 M-Coffe4ConsistencyNO43.60 PSI-CoffeeConsistencyProfile53.71 PROMALConsistencyProfile55.08 PROMAL-3DConsistencyPDB D-CoffeeConsistencyPDB61.00Expresso Score: fraction of correct columns when compared with a structure based reference (BB11 of BaliBase). Homology Extension
Method TemplateScoreComment ClustalW-2ProgressiveNO22.74 PRANKGapNO26.18Science2008 MAFFTIterativeNO26.18 MuscleIterativeNO31.37 ProbConsConsistencyNO40.80 ProbConsMonoPhasicNO37.53 T-CoffeeConsistencyNO42.30 M-Coffe4ConsistencyNO43.60 PSI-CoffeeConsistencyProfile53.71 PROMALConsistencyProfile55.08 PROMAL-3DConsistencyPDB D-CoffeeConsistencyPDB61.00Expresso Score: fraction of correct columns when compared with a structure based reference (BB11 of BaliBase). Structural Extension
T-Coffee and The World BLAST/ SOAP -Some Templates are obtained with a BLAST -Queries can be sent to the EBI or the NCBI -No Need for a Local BLAST installation Users sequences