29 mammalian genomes

Download 29 Mammalian Genomes

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  • 1.A High-Resolution Map of EvolutionaryConstraintIn the human genomeby Lindblad-Toh & colleagues, Nature 2011Presented by Nacho Caballero

2. Constrained DiversityIs the Key to Comparative Genomics 3. Percentage ofSites that Have1+ subsUndergone2+ subsSubstitutions 3+ subs 4+ subs 1 -0.5 - 0 -0.8 1.25 1.5 35 Average # of Subs. per Site (Branch Length) 4. Percentage of4 Genomes - 50 bp 0.8 subs/siteSites that HaveUndergone 1.25 subs/siteSubstitutions 1.5 subs/site 3 subs/site29 Genomes 12 bp 5 subs/site0.5 -0.3 -0.1 - 01 23 45 6Number of Neutral Substitutions per Site 5. Higher Resolution Uncovers Individual Binding SitesNPAS4bias4 genomes 29 genomes 6. Evolutionary Signatures HelpDiscover Novel GenesStop CodonsSynonymous SubstitutionFrame-Preserving IndelNon-Synonymous SubstitutionFrame-shifting IndelAnnotated as an Intronstartstop 7. Evolutionary Signatures HelpIdentify Stop-Codon Readthrough Stop CodonsSynonymous Substitution Frame-Preserving IndelNon-Synonymous Substitution Frame-shifting IndelSACM1L1st stop codon2nd stop codon 8. Evolutionary Signatures HelpIdentify Stop-Codon Readthrough 2nd stop codon1st stop codon 9. A Richer Picture of Conservation:Synonymous Constrained ElementsHOXA2 Basewise Conservation Synonymous Constrained Rate Enhancer Enhancer 10. A Richer Picture of Conservation: Codon-Specific Selection dN/dS > 1.5 Positive SelectiondN/dS = 1 Neutral Selection dN/dS < 0.5 Purifying Selection 11. A Richer Picture of Conservation: Codon-Specific Selection dN/dS > 1.5 Positive SelectiondN/dS = 1 Neutral Selection dN/dS < 0.5 Purifying Selection 12. A Richer Picture of Conservation: Codon-Specific Selection dN/dS > 1.5 Positive SelectiondN/dS = 1 Neutral Selection dN/dS < 0.5 Purifying Selection 13. 100-200 Mammalian Genomes Will Allow Single-Nt Resolution40% of the Constrained DiversityConstrained Genome Is the Key toIs Uncharted territory Comparative Genomics

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