13 Phylogenetics(I)

13 Phylogenetics(I) - 1 Introduction to Bioinformatics/...

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1 Introduction to Bioinformatics/ Elements of Bioinformatics Phylogenetics
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2 References Mount D.W. (2004) Bioinformatics: Sequence and Genome Analysis. 2nd ed. Cold Spring Harbor Lab. Press, N.Y. Chapter 7. Baxevanis, A.D., and Ouellette, B.F.F. (2005) Bioinformatics - A practical guide to the analysis of genes and proteins (3rd ed). John Wiley and Sons, NY. Chapter 14. • Baldauf SL (2003) Phylogeny for the faint of heart: a tutorial. Trends in Genetics 6:345-351. • Gregory T. R. (2008) Understanding Evolutionary Trees. Evo Edu Outreach 1:121–137.
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3 Uses of phylogenetics • Determine the evolutionary relationships among sequences or species as inferred from molecular data • Use in classification • For rapidly changing sequences, phylogenetic analysis can be used to track the spread of a virus through populations (molecular epidemiology) – e.g. Ou et al (1992) Science 256: 1165-1171 – e.g. Metzker ML (2002) PNAS 99: 14292-14297
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4 Phylogeny and classification of a protein family From: Bowles et al (2000) Phylogeny of the SOX family of developmental transcriptional factors based on sequence and structural indictors. Developmental Biology 227: 239-255.
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5 Phylogenetic tree to predict properties of an organism Pacific Yew ( Taxus brevifolia ) – produces Taxol for treating cancer European Yew ( Taxus baccata ) closely related to pacific yew – predicted to produce compounds related to Taxol
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6 (Human) (Human) (Civet) (Bat) (Bat) (Bat) Li W et al (2005) Bats are natural reservoirs of SARS-like coronaviruses. Science 310:676-9.
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This note was uploaded on 07/29/2010 for the course BIOC BIOC1805 taught by Professor Dr.brianwong during the Summer '09 term at HKU.

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13 Phylogenetics(I) - 1 Introduction to Bioinformatics/...

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