baca_lect - Building Phylogenies David Fernéndez—Baca...

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Unformatted text preview: Building Phylogenies David Fernéndez—Baca Depar’rmen’r of Compu’rer Science ISU Spring 2005 C0 Advanced T0 Phylogenetics: Phylog; ' Algofi ,_ ‘k ‘ .,. I: ....................................................................................................................................................................................................................... .. Alignments: Sparse Dynamic Programming Combined Alignment and Tree Construction Structural Alignment Protein Structure: Protein Folding Inverse Protein Folding Oliver Eulensfein :- i Dept. of Computer Science _ oeulensfecs . iast’afe. edu PhylogeneTic (evolu’rionary) Trees Describe evolu’rionar'y r'ela’rionships be’rween species H D 6 Go 0 Gi Canno’r be known wi’rh cer’rain’ry! Never’rheless, phylogenies can be useful ApplicaTions of PhylogeneTic Analysis - Inferring funcTion - Closely relaTed sequences occupy neighboring branches of Tree - Tracking changes in rapidly evolving popula’rions (e.g., viruses) - Which genes are under selecTion? Phyloinformm‘ics D ala [J 3393 - ComparaTive analysis Through phylogenies helps To undersTand biological funcTion ' ExploiT phylogenies for dam mining B C D 4-— Grau of 0193mm Disease Transmission and Medical Forensics Patient (3 Patient C Patient E Patient B Patient A Local Control 3 Local Control 2 Patient F Local Control 9 Local Control 35 Patient D g Discovering Snake AnTnn :fllank whip mane lelafir. rie'ue aria-:3 Carrr'mn b'cwn INEfiaarn h'cwn DLgLe Eel-en's $13113 Sun-Had thuk Butcr'e mam H r'g b'cwr Had-he lied hIH :k Beam ac der + Recommended Antwenene S-a'cl 3k "" E-SrrEII eyed make Australian mpue'lleau - Blackeneke T ger mafia - Death adder 'tOJEh scaled 51.3w - Tiger snake firmed-Pealde e'laqe Me’rhods for phylogeny cons’rruc’rion ° DisTonce—bosed - Porsimony ° Maximum likelihood Distance MaTr'ices 01234 5678 /—/> 1):er WSW? Mew/QM (100% Ultramefr'ic Matrices M a b O c 6 O C d 1010 0 a b c d d bi'zézié fl LeasT Squares DU- : dis’rcmce beTween i andj in maTrix Qr- / diJ- = dis’rance be’rween i and j in Tree ObjeTive: Find Tr'ee ThaT minimizes A 2 (DJ _dij)2 ‘ V lsi<an U 6 Characters A chorocTer can be a morphological TroiT or o lefier in a column of an alignment 0 b c f AC 6 a GT6 AX GTA GTA 6 ArfictWS 6‘ 9 + . 3L evoluM 7> Par'SImony g “1?st Goal: Find The Tree wi’rh leasT number a Markov models on Trees ° Observed: The species labeling The leaves . ® (@The ances’rral s’ra’res KN - Assumptions: - Only muTaTions are allowed YEA [‘5 - SiTes are independem‘ ,— _ C D - EvoluTion aT each siTe occurs according " ~ To a Maikov process x 9“ 7(1 , , , XK y l \/ 47 ~ W ]k Models of evoluTion (11‘ a siTe ° MuTaTion probabiliTy maTrix: ~3M : [mu], i,j E{A, C, T, G} where miJ- = Prob(i —>j muTaTion ir®fime uni’r) ° Differen’r branches of Tree may W d'ff n’rln’rhs l ere eg filflZe (X SAVE 3 The probabili’ry of an assigmenT : mTG ' mGA ' mGG 'mTT ' mTC 'mTT W L‘:\/ N M \f‘r \~ 1(«/ H Ances’rml recons’rruc’rion: mosT liker asignmenT * _ L - maxxyz {mxv ' myA ' mye 'mxz 'mzc 'mZT} KM Homology, or’rhology, and paralogy - Homology: Similari’ry a’r’rr'ibu’red To descen’r from a common ancesTor. - Orthologous sequences: Homologous sequences in differenT s ecies Tha’r arose from a common ances’rra gene during specia’rion. - may or may no’r be responsible for a similar func’rlon. - Paralogous sequences: Homologous sequences wu’rhln asmgle specues Tha’r arose by gene dUPlICCl'l'IOH. Or'Thology and Par'alogy hemolngs KI—’%. paruluge fregU. ehiekh’ menseri euseB chickfi frogB U. -ehain gene B-eha'm gene ram; dufiiicat-i—nnt/ early glebin gene hTTp://www.ncbi.n|m.nih.gov/EducaTion/BLASTinfo/Or’rho logy.h’rm| ...
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baca_lect - Building Phylogenies David Fernéndez—Baca...

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