T_Coffee.Overview - Growing Trees on the Right Compost...

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Growing Trees on the Right Compost Cédric Notredame Comparative Bioinformatics Group Bioinformatics and Genomics Program
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Manguel M, Samaniego F.J., Abraham Wald’s Work on Aircraft Suvivability, J. American Statistical Association. 79, 259-270, (1984)
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What ‘s in a Multiple Sequence Alignment Evolution Inertia Common Ancestry Shows up In the sequences Selection Important Features Are Preserved Functional Constraint Same Function Same Sequence Convergence Phylogenetic Footprint, Evolutionary Trace …
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Why So Much Interest For Multiple Alignments ? Extrapolation Motifs/Patterns Phylogeny Profiles Structure Prediction SNP Analysis Reactivity Analysis Regulatory Elements
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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…
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Producing The Right Alignment Multiple Sequence Alignments Influence Phylogenetic Trees Choice of Method is not Neutral Different Methods Different Alignments Different Trees Using The Right Models insures Producing the right Tree
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Model Based Alignments vs Naïve Alignments Naïve Alignment Lexicographic Alignment Maximizing the number of identities At best using a substitution matrix Model Based Alignments Using a model Protein structure information RNA Structure information Combining/Confronting Modeling methods Template based Alignments Model based Alignments through the use of Templates
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T-Coffee and Model Based Alignments T-Coffee Algorithm Expresso: Aligning Protein Structures R-Coffee: Aligning RNA structures M-Coffee: Combining methods
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T-Coffee: An extension of the progressive Alignment Algorithm
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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
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T-Coffee and Concistency… SeqA GARFIELD THE LAST F AT CAT Prim. Weight =88 SeqB GARFIELD THE F AST 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
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T-Coffee and Concistency… SeqA GARFIELD THE LAST F AT CAT Prim. Weight =88 SeqB GARFIELD THE F AST 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 F AT CAT Weight =88 SeqB GARFIELD THE F AST CAT --- SeqA GARFIELD THE LAST FA-T CAT Weight =77 SeqC GARFIELD THE VERY FAST CAT SeqB
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This note was uploaded on 04/06/2010 for the course COMPUTER S COMP5647 taught by Professor Dr.ping during the Spring '10 term at York University.

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T_Coffee.Overview - Growing Trees on the Right Compost...

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