MIT6_047f08_lec10_slide10

MIT6_047f08_lec10_slide10 - MIT OpenCourseWare...

Info iconThis preview shows pages 1–8. Sign up to view the full content.

View Full Document Right Arrow Icon
MIT OpenCourseWare http://ocw.mit.edu 6.047 / 6.878 Computational Biology: Genomes, Networks, Evolution Fall 2008 For information about citing these materials or our Terms of Use, visit: http://ocw.mit.edu/terms .
Background image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Molecular Evolution and Phylogenetics 6.047/6.878 - Computational Biology: Genomes, Networks, Evolution Lecture 11 Oct 7, 2008 Somewhere, something went wrong Patrick Winston’s 6.034
Background image of page 2
Challenges in Computational Biology DNA 4 Genome Assembly Gene Finding Regulatory motif discovery Database lookup Gene expression analysis 9 RNA transcript Sequence alignment Evolutionary Theory 7 T C ATG C TAT T CG TGATA A TGA G GATAT T T AT C ATAT T T ATGAT T T Cluster discovery 10 Gibbs sampling Protein network analysis 12 Emerging network properties 14 13 Regulatory network inference Comparative Genomics RNA folding
Background image of page 3

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Goals for today Basics of phylogeny Characters, traits, nodes, branches, lineages Gene trees, species trees Modeling sequence evolution Turning sequence data into distances Probabilistic models of nucleotide divergence Jukes-Cantor 1-parameter model, Kimura 2-parameter model From distances to trees Ultrametric, Additive, General Distances UPGMA, Neighbor Joining, guarantees and limitations Least-squared error, minimum evolution From alignments to trees Parsimony methods: set-based vs. dynamic programming Maximum likelihood methods MCMC and heuristic search
Background image of page 4
Open questions (?) • Panda – Bear or raccoon? • Out of Africa – mitochondrial evolution story? • Human evolution – Did we ever meet Neanderthal? • Primate evolution – Are we chimp-like or gorilla-like? • Vertebrate evolution – How did complex body plans arise? • Recent evolution – What genes are under selection?
Background image of page 5

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Inferring Phylogenies: Traits and Characters Trees can be inferred by several criteria: – Morphology data – Molecular data Kangaroo A C A G T G A C G CCCC AAA C G T Elephant A C A G T G A C G C T A C AAA C G T Dog CC T G T G A C G T AA C AAA C G A Mouse CC T G T G A C G T A G C AAA C G A Human CC T G T G A C G T A G C AAA C G A Image removed due to copyright restrictions.
Background image of page 6
Traits – as many as we have letters in DNA YAL042W -MKRSTLLSLDAFAKTEEDVRVRTRAGGLITLSCILTTLFLLVNEWGQFNSVVTRPQLVV candida586 MSSRPKLLSFDAFAKTVEDARIKTTSGGIITLICILITLVLIRNEYVDYTTIITRPELVV cdub17784 MSSRPKLLSFDAFAKTVEDARIKTTSGGIITLICILITLVLIRNEYVDYTTIITRPELVV cgla72177 -MKKSTLLSFDAFAKTEEDVRIRTRSGGFITLGCLVVTLMLLLSEWRDFNSVVTRPELVI cgui48535 -MPQPKLLSFDAFAKTVEDARVRTPAGGIITLICVIVVLYLIRNEYLEYTSIINRPELVV clus15345 MSSRPRLLSLDAFAKTVEDARVKTASGGVITLVCVLIVLFLIRNEYSDYMLVVVRPELVV ctro67868 MSSRPKLLSFDAFAKTVEDARIKTASGGIITLICVLITLILIRNEYIDYTTIITRPELVV klac20931 -MKKSPLLSIDAFGKTEEDVRVRTRTGGLITVSCIIITMLLLVSEWKQFSTIVTRPDLVV :. ***:***.** **.*::* :**.**: *:: .: *: .*: :: :: **:**: YAL042W DRDRHAKLELNMDVTFPSMPCDLVNLDIMDDSGEMQLDILDAGFTMSRLNSEG------R candida586 DRDINKQLDINLDISFINLPCDLISIDLLDVTGDLSLNIIDSGLKKIRLLKNKQGDVIVN cdub17784 DRDINKQLDINLDISFINLPCDLISIDLLDVTGDLSLNIIDSGLKKIRLLKNKQGDVIVN cgla72177 DRDRSLRLDLNLDITFPSMPCELLTLDIMDDSGEVQLDIMNAGFEKTRLSKEG------K cgui48535 DRDINKKLEINLDISFPDIPCDVLTMDILDVSGDLQVDLLLSGFEKFRLLKDG------L clus15345
Background image of page 7

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Image of page 8
This is the end of the preview. Sign up to access the rest of the document.

This note was uploaded on 09/24/2010 for the course EECS 6.047 / 6. taught by Professor Manoliskellis during the Fall '08 term at MIT.

Page1 / 46

MIT6_047f08_lec10_slide10 - MIT OpenCourseWare...

This preview shows document pages 1 - 8. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online