Integrating Biological Information In Multiple Sequence Alignments Confronting Bits and Pieces of Information Cédric Notredame CNRS-Marseille, France www.tcoffee.org.

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Presentation transcript:

Integrating Biological Information In Multiple Sequence Alignments Confronting Bits and Pieces of Information Cédric Notredame CNRS-Marseille, France

Building and Using Models Angstrom

Computing the Correct Alignement is a Complicated Problem

T-Coffee and Concistency…

Too Many Methods for ONE Alignment M-Coffee

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

Comparing Methods MAFFT

Going Further

Place your Bets…

Where to Trust Your Alignments Most Methods Agree Most Methods Disagree

When Sequences Are not Enough 3D-Coffee and Expresso

3D-Coffee: Combining Sequences and Structures Within Multiple Sequence Alignments

Expresso: Finding the Right Structure Template based Alignment of the Source Sequences Template-Source Alignment Why Not Using Structure Based Alignments

Expresso: Finding the Right Structure Sources Templates Template based Alignment of the Source Sequences Template-Source Alignment Library BLAST SAP Template Alignment Source Template Alignment Remove Templates Templates

3D-Coffee: Combining Sequences and Structures Within Multiple Sequence Alignments

Improving The Evaluation

More Than Structure based Alignments Structural Correctness Is Only the Easy Side of the Coin. In practice MSA are intermediate models used to generate other models: DataModel TypeBenchmark HomologyProfileYes EvolutionTreesNo Structure3D-StructureCASP FunctionAnnotationNo

Conclusion Template based Multiple Sequence Alignments Projecting any relevant information onto the sequences Using this Information Need for new evaluation procedures Functional Analysis Phylogenetic Analysis Homology Search (Profiles) Homology Modelling Integrating data  Making sure your bits of data can fight with one another

Fabrice Armougom (CNRS, FR) Sebastien Moretti (CNRS, FR) Olivier Poirot (CNRS, FR) Frederic Reinier (CRS4, IT) Karsten Suhre (CNRS, FR) Vladimir Saudek (Sanofi-Aventis, FR) Des Higgins (UCD, IE)h Orla O’Sullivan (UCD, IE) Iain Wallace (UCD, IE) Victor Jongeneel (SIB/VitalIT, CH) Bruno Nyfler (VitalIT, CH) Roger Hersch (EPFL, CH) Pierre Dumas (EPFL, CH) Basile Schaeli (EPFL, CH)

Turning Data into Models Data Columbus, considered that the landmass occupied 225°, leaving only 135° of water (Marinus of Tyre, 70 AD).Marinus of Tyre Columbus believed that 1° represented only 56 miles (Alfraganus, XIth century)Alfraganus He knew there was an island named Japan off the cost of China… Model Circumference of the Earth as 25,255 km at most, Canary Island to Japan : 3,700 km (Reality: 12,000 km.)

T-Coffee Results Validation Using BaliBase

Structures Vs Sequences

ClustalW: The Progressive Algorithm

The More Structures The Merrier Average Improvement over T-Coffee Struc/Seq Ratio

T-Coffee and Concistency… Each Library Line is a Soft Constraint (a wish) You can’t satisfy them all You must satisfy as many as possible (The easy ones)

Concistency Based Algorithms: T-Coffee Gotoh (1990) – Iterative strategy using concistency Martin Vingron (1991) – Dot Matrices Multiplications – Accurate but too stringeant Dialign (1996, Morgenstern) – Concistency – Agglomerative Assembly T-Coffee (2000, Notredame) – Concistency – Progressive algorithm ProbCons (2004, Do) – T-Coffee with a Bayesian Treatment

The Right Mixt of Methods

What’s in a Multiple Alignment? Structural Criteria – Residues are arranged so that those playing a similar role end up in the same column. Evolutive Criteria – Residues are arranged so that those having the same ancestor end up in the same column. Similarity Criteria – As many similar residues as possible in the same column

How Do We Perform In The Twilight Zone? Concistency Based Methods Have an Edge Hard to tell Methods Apart Sequence Alignment is NOT solved

T-Coffee and Concistency…

Three Types of Algorithms Progressive: ClustalW Iterative: Muscle Concistency Based: T-Coffee and Probcons

3D-Coffee: Combining Sequences and Structures Within Multiple Sequence Alignments

What’s in a Multiple Alignment? The MSA contains what you put inside: – Structural Similarity – Evolutive Similarity – Sequence Similarity You can view your MSA as: – A record of evolution – A summary of a protein family – A collection of experiments made for you by Nature…