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194 Pages

### Slides8

Course: STA 294, Fall 2008
School: Duke
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Word Count: 1404

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comparison Pairwise table Calculate all pairwise alignment scores and arrange them in a table S1 S2 S3 S4 S5 2 0 9 1 S1 10 5 4 S2 10 25 8 S3 5 25 11 S4 4 8 11 S5 2 0 9 1 Convert all score into distances ... 1. FengDoolitle : D=log(SSrand)/(SmaxSrand) 2. Model based distances log det formular maximum likelihood root S9 S6 S8 S9 S2 S3 S4 S1 S5 S6 S2 S3 S5 S7 S7 S8 S4 S1 Progressive Profile Alignment...

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comparison Pairwise table Calculate all pairwise alignment scores and arrange them in a table S1 S2 S3 S4 S5 2 0 9 1 S1 10 5 4 S2 10 25 8 S3 5 25 11 S4 4 8 11 S5 2 0 9 1 Convert all score into distances ... 1. FengDoolitle : D=log(SSrand)/(SmaxSrand) 2. Model based distances log det formular maximum likelihood root S9 S6 S8 S9 S2 S3 S4 S1 S5 S6 S2 S3 S5 S7 S7 S8 S4 S1 Progressive Profile Alignment Build Profiles freeze alignments optimal profile alignment ClustalW Thompson Higgins Gibson 1994 Put together some good ideas: Distances of pairs of sequences are based on a full stochastic model of sequence evolution (... to be discussed soon) The guide tree is computed by a valid method of phylogenetic tree reconstruction Saitou and Nei 1987 The multiple alignment is put together by progressive profile alignment Sequence weighting is applied Gaussian branching processes Altschul Carroll Lipman 1989 Contributions from biology: Score matrices influence the alignment results. The score matrix used to score pairwise alignments is chosen on the basis of the evolutionary distance of the sequences. Different matrices for closely related sequences and remote pairs of sequences. The hydrophobic core of a protein is more conserved than its surface. Position specific gapopen profile penalties are multiplied by a modifier that is a function of the residues observed at the position. Hydrophobic residues (which are more likely to be in the well conserved core of the protein) give higher gap penalties than hydrophilc residues (which are more likely to be on the water accesible and less conserved surface of the protein) Loops on the surface of a protein are often missing in other members of a protein family. Gap open penalties are also decreased if the position is spanned by a consecutive strech of five or more hydrophilic residues. Insertions and deletions are rare events, but once they occur, they are propagated and show up in many family members at the same position. Both gapopen and gapextend penalties are increased if there are no gaps in a column but gaps occur nearby in the partial alignments. This tries to enforce that gaps show up at the same position. A pairwise alignment whispers, a full multiple alignment shouts out loud. In the progressive alignment stage, if the score of a profile alignment is low, the guide tree may be adjusted on the fly to defer the low scoring alignment until later when more profile information has been accumulated. ...along the same lines: Early decissions might be wrong since there was little profile information available at this time. Remove the first sequence from the alignment and realign it to the almost full alignment using sequence to profile alignment. Continue with the second, third ,... sequence. Iterate for some time. (not implemented in ClustalW) 6 & 2 s r q p p %D ` & ` Aai0 h e% \$ 2 # 0 ) ) 7 1 ) h D D B ) 1 # ) H0 ` 4 %5\$ 6 D 4 & b D 4 2 D g b # ) D D f 2 ) b & 4 D AeG5\$ US4 A# G0 5eG6 %" ! \$ # b b D 1 0 4 2 D c 4 0 b 0 ' & ' # T & XA5\$ d I Ga(A5\$ ` 2 D ) \$ 7 # 30 WYAX1 W@0 V US3I HG# 4 ) \$ B ) ) T R Q Q P E D D B 2 # 0 4 1 7 6 # \$ 4 2 1 0 & F) CA@98530 ) (' & %" ! \$ # 0.9 0.9 0.02 A 0.02 0.06 T 0.06 0.06 Purines A,G Pyrimidines C,T 0. 02 0.06 0. 02 0. 02 0.02 G 0.02 0.9 C 0.9 No Action 0.9 Transition 0.06 Transversion 0.02 0. 02 SS G S S G S G 0) U8W85g ) D b ' & 0 \$ & 4 # ) U2 0 5%US4 X9AD (%e5%# V AaW%D ` D \$ D f D 1 2 \$ D g D \$ 4 2 D 0 \$ D f 2 0 # D 7 2 0 4 2 # D US4 '3GG6 U3AX1 (& %(S4 a%3) & 4 & f D 7 ) # ! & b D D \$ " ! " ! 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D g & D D %(f (& b ` & D \$ 7 YA# 2 ! A3W(6 85) 2 # 0...

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STA2444/23/2003Take Home Final ExamDue 5/1/2003 by 5pm This is an open note/open book test. All work must be your own.Study of the growth of plants can be a crucial element in understanding how they compete for resources. For example, soybean
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ill sandwich &quot;Yes&quot; &quot;Yes&quot; &quot;Yes&quot; &quot;Yes&quot; &quot;Yes&quot; &quot;Yes&quot; &quot;Yes&quot; &quot;Yes&quot; &quot;Yes&quot; &quot;Yes&quot; &quot;Yes&quot; &quot;Yes&quot; &quot;Yes&quot; &quot;Yes&quot; &quot;Yes&quot; &quot;Yes&quot; &quot;Yes&quot; &quot;Yes&quot;
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exposure nma &quot;high&quot; 28 &quot;high&quot; 35 &quot;high&quot; 37 &quot;high&quot; 37 &quot;high&quot; 43.5 &quot;high&quot; 44 &quot;high&quot; 45.5 &quot;high&quot; 46 &quot;high&quot; 48 &quot;high&quot; 48.
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subject fev1 gender 1 2.30 0 2 2.15 1 3 3.50 1 4 2.60 0 5 2.75 0 6 2.82 1 7 4.05 1 8 2.25 1 9 2.68 0
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x1 x2 y1 y2 y3 y4 10 8 8.04 9.14 7.46 6.58 8 8 6.95 8.14 6.77 5.76 13 8 7.58 8.74 12.74 7.71 9 8 8.81 8.77 7.11 8.84 11 8 8.33 9.26 7.81 8.47 14 8 9.96 8.1 8.84 7.04 6 8 7.24 6.13 6.08 5.25 4 19 4.26 3.1 5.39 12.5 12 8 10.84 9.13 8.15 5.56
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D m S WS y 0 10 1 3408 623 0.04 5 1 206.8 680.2 0.1 5 1 1841.2 721.4 0.16 5 1 1223.2 750.4 0.28 5 1 861.2 789.4 0.04 5 2 2810.8 672.2 0.1 5 2 860.8 709.2 0.16 5 2 592.8 731.2 0.28 5 2 2642.8 778.2 0.04 5 3 2399.2 668.4 0.1 5 3 327.2 715.6
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Pressure Temp 20.79 194.5 20.79 194.3 22.4 197.9 22.67 198.4 23.15 199.4 23.35 199.9 23.89 200.9 23.99 201.1 24.02 201.4 24.01 201.3 25.14 203.6 26.57 204.6 28.49 209.5 27.76 208.6 29.04 210.7 29.88 211.9 30.06 212.2
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Min. 1st Qu. Median Mean 3rd Qu. Max. 41 76 89 85.28 96 100 Decimal point is 1 place to the right of the colon 4 : 14 4 : 5 : 5 : 55 6 : 1 6 : 55569 7 : 0011123333444
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Lauren Rocheleau Sajid Sharif Dan Southam Brian YehBME 265.9 Duke University Dr. TruskeyOutlineBackground Biological Previous DeviceObjectives Goal Statement Functional SpecificationsPrototype Design Mechanical ElectricalPrototype Ev
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Aerosolized Drug Delivery ChamberBME 227 Design in Biotechnology Professor: Dr. Aura Gimm Client: Dr. William Steinbach April 24, 2007 Bill Monaco Emily Schmidt Todd Seaver Yuxuan HuOverviewBackground Client Requirements Original design Improved
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Cell ChamberClient: Dr.SettonLeader: Alvin Kpaeyeh Web/Archivist: Lucy He Materials: Brendan Casey Communications: Jenna OlsonOverview Problem Statement Background Product Design Specifications Design Alternatives Future Outlook Challenges
Duke - BME - 227
Device for Dynamic Pressurization of Arteries and Strain Measurement : Mr. ArteryJay Crowley Jim Kragel Phil Kragel Ethan PuchatyOriginal Problem StatementThere is increasing evidence that wall mechanical forces play a role in the progression of
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Home Intraocular Pressure Measurement DeviceTeam: Priya Karani, Shawn Tan, Lin Xiong, &amp; Cen Zhang Clients: Richard Awdeh, MD and Felix Chau, MD Duke University Eye CenterBME 227L Professor Aura Gimm February 10, 2006Abstract Glaucoma is the sec
Duke - BME - 227
Design of an Aseptic Thymus Slicing DeviceCarolyn Eagan Richard Lee Marcus Reeslund Rachel WerginFebruary 9, 2006 BME 227: Design in BiotechnologyDesign of an Aseptic Thymus Slicing DeviceCarolyn Eagan, Richard Lee, Marcus Reeslund and Rachel