p(-,i)+p(,i)+p(-,v)+p(i,v),v)+p(i,v)
|
|
- Edith Wright
- 5 years ago
- Views:
Transcription
1 Multile Sequence Alignment Given: Set of sequences Score matrix Ga enalties Find: Alignment of sequences such that otimal score is achieved. Motivation Aligning rotein families Establish evolutionary relationshis Identify imortant functional regions Yield structural clues Aligning non-coding DNA sequences Find conserved regions in DNA for control of exression Infer evolutionary relationshis Identify imortant functional regions Motivation Scoring a Multile Alignment Binding sites, DNA sequence motifs, may be conserved within secies (to control exression in concerted fashion) The sites may be conserved across secies (using similar control mechanisms) May diverge within and across secies for secial urose or evolutionary drift S: GA_TCA : GTCTGA : GATATT Scoring a Multile Alignment Alignment score = sum of column scores Identify a reasonable method of obtaining a cumulative score for substitutions in each column is a challenge. Column score: I V - I I I V - SP (Sum of Pairs) measure (oular method): Comute airwise scores of all airs and sum them SP-score(I, score(i,-,i,v),i,v) = (I,-)+(I,I)+(I,V)+ (-,I)+(,I)+(-,V)+(I,V),V)+(I,V) Ga enalty constant or linear or nonlinear (affects the comutational comlexity). (-,-) =?0 SP-score( score(α) = Σ score(α ij where α ij is the airwise alignment induced by α on sequences s i, s j.
2 Ex. A Problem with SP-score N-N N match N-C match Score (BLOSUM2) Sequence Column A Column B Column C A B C N N N CN (3N-N(), N(), C-C(9)) C(9)) 9 The scores decrease raidly! SP-score tends to overweight the influence of mutations. -3 N A Problem with SP-score Sequence Column A 2 n s(n,n) =, s(n,c)= 3; Score of the column A = Score of the column B = Column B Column C n(n-)/2 n(n-)/2 9(n-) Relative difference: 9(n-)/[n(n-)/2] = 3/n (inverse deendence on n) Counter-intuitive: relative diff should be increase with the more evidence we have for a conserved asaragine N. Multile Alignments: Scoring Sum of airs (SP-Score) Score) Number of matches (multile longest common subsequence score) Entroy score Multile LCS Score A column is a match if all the letters in the column are the same AAA AAA AAT ATC Only good for very similar sequences Methods for Multile Alignment Dynamic Programming Progressive Alignment Star CLUSTALW Iterative Alignment Hidden Markov Model s s2 s3 Aligning Three Sequences GATTCA GTCTGA GATATT 2
3 Aligning Three Sequences Same strategy as aligning two sequences Use a 3-D Manhattan Cube, with each axis reresenting a sequence to align For global alignments, go from source to sink source W 2-D vs 3-D Alignment Grid V 2-D edit grah sink 3-D edit grah 2-D cell versus 3-D Alignment Cell Architecture of 3-D Alignment Cell (i-,j-,k-) (i-,j-,k) (i-,j,k-) (i-,j,k) In 2-D, 3 edges in each unit square? In 3-D, 7 edges in each unit cube (i,j-,k-) (i,j-,k) (i,j,k-) (i,j,k) Alignment Paths Multile Alignment: Dynamic Programming A -- T G C A A T -- C A T G C x coordinate y coordinate z coordinate Resulting ath in (x,y,z) sace: (0,0,0) (,,0) (,2,) (2,3,2) (3,3,3) (,,) s i,j,k = max s i-,j-,k- + δ(v i, w j, u k ) s i-,j-,k + δ (v i, w j, _ ) s i-,j,k- + δ (v i, _, u k ) s i,j-,k- + δ (_, w j, u k ) s i-,j,k + δ (v i, _, _) s i,j-,k + δ (_, w j, _) s i,j,k- + δ (_, _, u k ) cube diagonal: no indels face diagonal: one indel edge diagonal: two indels (x, y, z) is an entry in the 3-D scoring matrix 3
4 Multile Alignment: Running Time For 3 sequences of length n,, the run time is 7n 3 ; O(n 3 ) For k sequences, build a k-dimensional Manhattan, with run time (2 k -)( )(n k ); O(2 k n k ) Progressive Alignment Star method CLUSTALW Conclusion: dynamic rogramming aroach for alignment between two sequences is easily extended to k sequences but it is imractical due to exonential running time Multile Alignment Induces Pairwise Alignments Reverse Problem: Constructing Multile Alignment from Pairwise Alignments Every multile alignment induces airwise alignments Induces: x: AC-GCGG-C y: AC-GC-GAGGAG z: GCCGC-GAGGAG x: ACGCGG-C; C; x: AC-GCGG-C; C; y: AC-GCGAG y: ACGC-GAC; GAC; z: GCCGC-GAG; GAG; z: GCCGCGAG Given 3 arbitrary airwise alignments: x: ACGCTGG-C; C; x: AC-GCTGG-C; C; y: AC-GC-GAGGAG y: ACGC--GAC; z: GCCGCA-GAG; GAG; z: GCCGCAGAG can we construct a multile alignment that induces them? NOT ALWAYS The STAR Alignment Method Using a airwise alignment method find the sequence that is most similar to all the other sequences: score(α i ) = Σ score(α Using this best sequence as the center (of a star, hence the name) align the other sequences following the once a ga always a ga rule. Ex: S S S5 A T T G C C A T T A T G G C C A T T A T C C A A T T T T A T C T T C T T A C T G A C C More on STAR Alignment Assuming similarity matrix for the airwise comaring of the sequences: S S S5 Σscore( score(α ij S S S Choose s be the center of the Star! S5 S S
5 More on STAR Alignment Next we get the best alignment between S and the other sequences as follows: S A T T G C C A T T A T G G C C A T T S A T T G C C A T T - - A T C - C A A T T T T S A T T G C C A T T S A T C T T C - T T S A T T G C C A T T S5 A C T G A C C - - More on STAR Alignment Build the MSA starting with S? and : A T T G C C A T T A T G G C C A T T Adding using once a ga always a ga A T T G C C A T T - - A T G G C C A T T - - A T C - C A A T T T T Reeat to include all the sequences A T T G C C A T T - - A T G G C C A T T - - A T C - C A A T T T T A T C T T C - T T - - A C T G A C C Comlexity of STAR Alignment Clearly, the time comlexity of the STAR method is dominated by comuting the airwise alignment. For k sequences, there are O(k 2 ) airs Each airwise alignment takes O(n 2 ), n = length of each seq. Cost for comuting all airwise alignments: O((kn) 2 ) Cost to merge the sequences into a msa. If n max is the uer bound of the alignment length, one merge takes O(kn max ). Total takes O(k 2 n max ). The total time comlexity for STAR method: O( k 2 n 2 + k 2 n max ) Profile Alignment Problem with Star aroach --- all alignment are determined by airwise sequence alignments. Profile alignment uses osition-secificsecific information from grou s multile alignment to align a new sequence to it. Mismatches at highly conserved ositions should be enalized more Gas should be enalized more at ositions where few gas occur Scoring function SP-score Profile Alignment Aligning two multile alignment (rofiles) using SP-score.. A T T G C C A T T k+. A T C - C A A T k. A T G G C C A T T K. A - C T G A A C Recall: SP-score( score(α ) = Σ score(α ij SP-score( score(α) = Σ SP-score( score(α ) SP-score( score(α) = Σ SP-score( score(α ) = ΣΣ score(α ij = ΣΣ score(α + ΣΣ score(α + Σ Σ score(α ij k k< i k k<j K The alignment can be done exactly like a standard airwise alignment! Need to be otimized CLUSTALW CLUSTALW is a rogressive method use a airwise alignment method to determine the most related sequences rogressively add less related sequences or grous of sequences to the initial alignment CLUSTAL family CLUSTAL - gives equal weight to all sequences CLUSTALW - can give different weights to the sequences & other rogram arameters CLUSTALX - rovides a GUI to CLUSTAL 5
6 CLUSTALW Construct a distance matrix of all k(k )/2 airs by airwise dynamic rogramming alignment and comute the distances between all air sequences (-distance: the roortion () of nucleotide sites at which two sequences being comared are different). Construct a guide tree by a neighbor-joining clustering algorithm Progressively align at nodes in order of decreasing similarity, using sequence-sequence, sequence, sequence-rofile, and rofile-rofile alignment More on CLUSTALW After comuting the distance between all airs of sequences we ut them into a matrix. For examle if we consider a set of 7 sequences we could have the following matrix: Seq. S S - S S5 S S S S S S Neighbor Joining Very oular method! Assumes additivity: distance between airs of leaves = sum of lengths of edges connecting them Produces unrooted tree Very much like the Fitch-Margoliash method, excet that the choice as to which sequence to air is done differently 3 Neighbor Joining Additivity: distance between airs of leaves equals to the sum of lengths of edges connecting them. d km = (d im + d jm d ij ( k = arent of i & j ) How to choose the neighbor leaves? /2. Neighbor Joining Find the modified distance matrix: Find the sum of the distance between seq i and all other sequences: r i = Σ k d ik / (n 2), (n = total # of seqs) Find the modified distance matrix: D ij = d ij ( r i + r j ), Claim: A air of leaves i, j for which D ij is minimal will be neighboring leaves. Algorithm: Neighbor Joining Initialization Define T to be the set of leaf nodes, one for each given seq Let L = T Iteration: Pick i, j in L for which D ij is the minimal Define a new node k and set d km =(d im +d jm d /2, m in L Add k to T with edges of lengths d ik =(d ij +r i r j )/2, d jk =d ij - d ik Remove i and j from L and add k Termination: When L consists of two leaves i and j add the remaining edge between i and j,, with length d ij
7 d D Examle d ik =(d ij +r i r )/2, j d jk =d ij - d ik 0. 5 d km =(d im +d jm d /2 d D d Profile Alignment Aligning two multile alignment (rofiles) using SP-score.. A T T G C C A T T k+. A T C - C A A T k. A T G G C C A T T K. A - C T G A A C Recall: SP-score( score(α ) = Σ score(α ij SP-score( score(α) = Σ SP-score( score(α ) SP-score( score(α) = Σ SP-score( score(α ) = ΣΣ score(α ij = ΣΣ score(α + ΣΣ score(α + Σ Σ score(α ij k k< i k k<j K The alignment can be done exactly like a standard airwise alignment! Need to be otimized s s2 s3 s GTTGA GTTTGA GATATT GTATA Exercise Distances -distance: For a airwise alignment, count the number of mismatches/gas between the two sequences, then divide this value by the length of the alignment. Ex. N K L - O N distance = 3/ =.5 - M L N O N Jukes-Cantor distance d = (¾)log[-(/3)](/3)] =-distance More on CLUSTALW Construct a guide tree using Neighbor Joining method. For the distance matrix in the examle we could construct the following guide tree. S S S S S5 7
8 More on CLUSTALW Progressively align at nodes in order of decreasing similarity, using sequence-sequence, sequence, sequence-rofile, and rofile-rofile alignment In our examle we first align S with (grou) then with S (grou2), then align grou with grou2, then we continue until we have only one alignment. CLUSTALW htt://clustalw.genome.j/ Ex: (FASTA format) >seqa GARFIELDTHEFASTCAT >seqb GARFIELDTHEVERYFASTCAT >seqc GARFIELDTHEFATCAT Problem of Sequence Weights The available sequences are not randomly samled, but reflect biases in how we collect sequences. If weight everything equally, then closely related sequences will be allowed to dominate the multile alignment. As a result, conclusions about ) conservation, 2) evolutionary distance, 3) reliability of redictions would be wrong. Sequence Weighting Examle CYEGNGHF Human- CYEGNGDF Human-2 CYHGNGDF Human-2 CYHGNGDS Mouse CYHGNGQS Rat CFEGNGHS Pig Solutions: don t weight the three humans equally with the others. Use a measure of similarity to down-weight weight their influence on the multile alignment. More on CLUSTALW More heuristics of CLUSTALW: Sequences are weighted to comensate for biased reresentation in large subfamilies and the defects of the sum-of-airs. Use different substitution matrix (BLOSUM80 for closely related sequences; BLOSUM50 for distant sequences) Set ga enalty be a function of the residues observed at the osition (hydrohobic residues give higher ga enalties than hydrohilic or flexible residues) Set ga and ga extension enalties to force all the gas to occur in the same laces ClustalW In Summary Poular multile alignment tool today W stands for weighted (different arts of alignment are weighted differently). Three-ste rocess ) Construct airwise alignments 2) Build Guide Tree 3) Progressive Alignment guided by the tree 8
9 Iterative Methods Shortcoming of Progressive Aroach: Deendence uon initial alignments Sub-alignments are frozen frozen Errors in alignment roagated Iterative Methods: Begin with an initial alignment A sequence or a grou of sequences is taken out and realigned to a rofile of the remaining aligned sequences. Alignment is reeatedly refined until the alignment does not change. 9
Multiple Sequence Alignment
Multiple Sequence Alignment Multiple Alignment versus Pairwise Alignment Up until now we have only tried to align two sequences. What about more than two? And what for? A faint similarity between two sequences
More informationMultiple Sequence Alignment
Multiple Sequence Alignment Multiple Alignment versus Pairwise Alignment Up until now we have only tried to align two sequences.! What about more than two? And what for?! A faint similarity between two
More informationQuantifying sequence similarity
Quantifying sequence similarity Bas E. Dutilh Systems Biology: Bioinformatic Data Analysis Utrecht University, February 16 th 2016 After this lecture, you can define homology, similarity, and identity
More information5. MULTIPLE SEQUENCE ALIGNMENT BIOINFORMATICS COURSE MTAT
5. MULTIPLE SEQUENCE ALIGNMENT BIOINFORMATICS COURSE MTAT.03.239 03.10.2012 ALIGNMENT Alignment is the task of locating equivalent regions of two or more sequences to maximize their similarity. Homology:
More informationMultiple Alignment. Slides revised and adapted to Bioinformática IST Ana Teresa Freitas
n Introduction to Bioinformatics lgorithms Multiple lignment Slides revised and adapted to Bioinformática IS 2005 na eresa Freitas n Introduction to Bioinformatics lgorithms Outline Dynamic Programming
More informationLecture 14: Multiple Sequence Alignment (Gene Finding, Conserved Elements) Scribe: John Ekins
Lecture 14: Multiple Sequence Alignment (Gene Finding, Conserved Elements) 2 19 2015 Scribe: John Ekins Multiple Sequence Alignment Given N sequences x 1, x 2,, x N : Insert gaps in each of the sequences
More informationCopyright 2000 N. AYDIN. All rights reserved. 1
Introduction to Bioinformatics Prof. Dr. Nizamettin AYDIN naydin@yildiz.edu.tr Multiple Sequence Alignment Outline Multiple sequence alignment introduction to msa methods of msa progressive global alignment
More informationLearning Sequence Motif Models Using Gibbs Sampling
Learning Sequence Motif Models Using Gibbs Samling BMI/CS 776 www.biostat.wisc.edu/bmi776/ Sring 2018 Anthony Gitter gitter@biostat.wisc.edu These slides excluding third-arty material are licensed under
More informationTHEORY. Based on sequence Length According to the length of sequence being compared it is of following two types
Exp 11- THEORY Sequence Alignment is a process of aligning two sequences to achieve maximum levels of identity between them. This help to derive functional, structural and evolutionary relationships between
More informationTree of Life iological Sequence nalysis Chapter http://tolweb.org/tree/ Phylogenetic Prediction ll organisms on Earth have a common ancestor. ll species are related. The relationship is called a phylogeny
More informationSequence Analysis '17- lecture 8. Multiple sequence alignment
Sequence Analysis '17- lecture 8 Multiple sequence alignment Ex5 explanation How many random database search scores have e-values 10? (Answer: 10!) Why? e-value of x = m*p(s x), where m is the database
More informationPhylogenetic Tree Reconstruction
I519 Introduction to Bioinformatics, 2011 Phylogenetic Tree Reconstruction Yuzhen Ye (yye@indiana.edu) School of Informatics & Computing, IUB Evolution theory Speciation Evolution of new organisms is driven
More informationFeedback-error control
Chater 4 Feedback-error control 4.1 Introduction This chater exlains the feedback-error (FBE) control scheme originally described by Kawato [, 87, 8]. FBE is a widely used neural network based controller
More informationMultiple Sequence Alignment
Multiple Sequence Alignment BMI/CS 576 www.biostat.wisc.edu/bmi576.html Colin Dewey cdewey@biostat.wisc.edu Multiple Sequence Alignment: Tas Definition Given a set of more than 2 sequences a method for
More informationLecture 4: Evolutionary Models and Substitution Matrices (PAM and BLOSUM)
Bioinformatics II Probability and Statistics Universität Zürich and ETH Zürich Spring Semester 2009 Lecture 4: Evolutionary Models and Substitution Matrices (PAM and BLOSUM) Dr Fraser Daly adapted from
More informationCONCEPT OF SEQUENCE COMPARISON. Natapol Pornputtapong 18 January 2018
CONCEPT OF SEQUENCE COMPARISON Natapol Pornputtapong 18 January 2018 SEQUENCE ANALYSIS - A ROSETTA STONE OF LIFE Sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of
More informationOutline. Markov Chains and Markov Models. Outline. Markov Chains. Markov Chains Definitions Huizhen Yu
and Markov Models Huizhen Yu janey.yu@cs.helsinki.fi Det. Comuter Science, Univ. of Helsinki Some Proerties of Probabilistic Models, Sring, 200 Huizhen Yu (U.H.) and Markov Models Jan. 2 / 32 Huizhen Yu
More informationBioinformatics 1. Sepp Hochreiter. Biology, Sequences, Phylogenetics Part 4. Bioinformatics 1: Biology, Sequences, Phylogenetics
Bioinformatics 1 Biology, Sequences, Phylogenetics Part 4 Sepp Hochreiter Klausur Mo. 30.01.2011 Zeit: 15:30 17:00 Raum: HS14 Anmeldung Kusss Contents Methods and Bootstrapping of Maximum Methods Methods
More informationComputer arithmetic. Intensive Computation. Annalisa Massini 2017/2018
Comuter arithmetic Intensive Comutation Annalisa Massini 7/8 Intensive Comutation - 7/8 References Comuter Architecture - A Quantitative Aroach Hennessy Patterson Aendix J Intensive Comutation - 7/8 3
More information2. Sample representativeness. That means some type of probability/random sampling.
1 Neuendorf Cluster Analysis Assumes: 1. Actually, any level of measurement (nominal, ordinal, interval/ratio) is accetable for certain tyes of clustering. The tyical methods, though, require metric (I/R)
More informationMODELING THE RELIABILITY OF C4ISR SYSTEMS HARDWARE/SOFTWARE COMPONENTS USING AN IMPROVED MARKOV MODEL
Technical Sciences and Alied Mathematics MODELING THE RELIABILITY OF CISR SYSTEMS HARDWARE/SOFTWARE COMPONENTS USING AN IMPROVED MARKOV MODEL Cezar VASILESCU Regional Deartment of Defense Resources Management
More informationMolecular Evolution and Phylogenetic Tree Reconstruction
1 4 Molecular Evolution and Phylogenetic Tree Reconstruction 3 2 5 1 4 2 3 5 Orthology, Paralogy, Inparalogs, Outparalogs Phylogenetic Trees Nodes: species Edges: time of independent evolution Edge length
More information"Nothing in biology makes sense except in the light of evolution Theodosius Dobzhansky
MOLECULAR PHYLOGENY "Nothing in biology makes sense except in the light of evolution Theodosius Dobzhansky EVOLUTION - theory that groups of organisms change over time so that descendeants differ structurally
More informationEVOLUTIONARY DISTANCES
EVOLUTIONARY DISTANCES FROM STRINGS TO TREES Luca Bortolussi 1 1 Dipartimento di Matematica ed Informatica Università degli studi di Trieste luca@dmi.units.it Trieste, 14 th November 2007 OUTLINE 1 STRINGS:
More informationThe vast amount of sequence data collected over the past two
Local grah alignment and motif search in biological networks Johannes Berg and Michael Lässig Institut für Theoretische Physik, Universität zu Köln, Zülicherstrasse 77, 50937 Cologne, Germany Edited by
More informationPhylogenetics: Distance Methods. COMP Spring 2015 Luay Nakhleh, Rice University
Phylogenetics: Distance Methods COMP 571 - Spring 2015 Luay Nakhleh, Rice University Outline Evolutionary models and distance corrections Distance-based methods Evolutionary Models and Distance Correction
More informationSystem Reliability Estimation and Confidence Regions from Subsystem and Full System Tests
009 American Control Conference Hyatt Regency Riverfront, St. Louis, MO, USA June 0-, 009 FrB4. System Reliability Estimation and Confidence Regions from Subsystem and Full System Tests James C. Sall Abstract
More informationSequence Analysis 17: lecture 5. Substitution matrices Multiple sequence alignment
Sequence Analysis 17: lecture 5 Substitution matrices Multiple sequence alignment Substitution matrices Used to score aligned positions, usually of amino acids. Expressed as the log-likelihood ratio of
More informationFE FORMULATIONS FOR PLASTICITY
G These slides are designed based on the book: Finite Elements in Plasticity Theory and Practice, D.R.J. Owen and E. Hinton, 1970, Pineridge Press Ltd., Swansea, UK. 1 Course Content: A INTRODUCTION AND
More informationTowards understanding the Lorenz curve using the Uniform distribution. Chris J. Stephens. Newcastle City Council, Newcastle upon Tyne, UK
Towards understanding the Lorenz curve using the Uniform distribution Chris J. Stehens Newcastle City Council, Newcastle uon Tyne, UK (For the Gini-Lorenz Conference, University of Siena, Italy, May 2005)
More informationModel checking, verification of CTL. One must verify or expel... doubts, and convert them into the certainty of YES [Thomas Carlyle]
Chater 5 Model checking, verification of CTL One must verify or exel... doubts, and convert them into the certainty of YES or NO. [Thomas Carlyle] 5. The verification setting Page 66 We introduce linear
More informationHotelling s Two- Sample T 2
Chater 600 Hotelling s Two- Samle T Introduction This module calculates ower for the Hotelling s two-grou, T-squared (T) test statistic. Hotelling s T is an extension of the univariate two-samle t-test
More informationFinite-State Verification or Model Checking. Finite State Verification (FSV) or Model Checking
Finite-State Verification or Model Checking Finite State Verification (FSV) or Model Checking Holds the romise of roviding a cost effective way of verifying imortant roerties about a system Not all faults
More informationUniversal Finite Memory Coding of Binary Sequences
Deartment of Electrical Engineering Systems Universal Finite Memory Coding of Binary Sequences Thesis submitted towards the degree of Master of Science in Electrical and Electronic Engineering in Tel-Aviv
More informationOverview Multiple Sequence Alignment
Overview Multiple Sequence Alignment Inge Jonassen Bioinformatics group Dept. of Informatics, UoB Inge.Jonassen@ii.uib.no Definition/examples Use of alignments The alignment problem scoring alignments
More informationPhylogenetic analyses. Kirsi Kostamo
Phylogenetic analyses Kirsi Kostamo The aim: To construct a visual representation (a tree) to describe the assumed evolution occurring between and among different groups (individuals, populations, species,
More informationCh. 9 Multiple Sequence Alignment (MSA)
Ch. 9 Multiple Sequence Alignment (MSA) - gather seqs. to make MSA - doing MSA with ClustalW - doing MSA with Tcoffee - comparing seqs. that cannot align Introduction - from pairwise alignment to MSA -
More informationAnalysis of some entrance probabilities for killed birth-death processes
Analysis of some entrance robabilities for killed birth-death rocesses Master s Thesis O.J.G. van der Velde Suervisor: Dr. F.M. Sieksma July 5, 207 Mathematical Institute, Leiden University Contents Introduction
More informationElementary Analysis in Q p
Elementary Analysis in Q Hannah Hutter, May Szedlák, Phili Wirth November 17, 2011 This reort follows very closely the book of Svetlana Katok 1. 1 Sequences and Series In this section we will see some
More informationAnalysis of Group Coding of Multiple Amino Acids in Artificial Neural Network Applied to the Prediction of Protein Secondary Structure
Analysis of Grou Coding of Multile Amino Acids in Artificial Neural Networ Alied to the Prediction of Protein Secondary Structure Zhu Hong-ie 1, Dai Bin 2, Zhang Ya-feng 1, Bao Jia-li 3,* 1 College of
More informationBayesian Networks Practice
Bayesian Networks Practice Part 2 2016-03-17 Byoung-Hee Kim, Seong-Ho Son Biointelligence Lab, CSE, Seoul National University Agenda Probabilistic Inference in Bayesian networks Probability basics D-searation
More informationMODEL-BASED MULTIPLE FAULT DETECTION AND ISOLATION FOR NONLINEAR SYSTEMS
MODEL-BASED MULIPLE FAUL DEECION AND ISOLAION FOR NONLINEAR SYSEMS Ivan Castillo, and homas F. Edgar he University of exas at Austin Austin, X 78712 David Hill Chemstations Houston, X 77009 Abstract A
More informationAn Improved Calibration Method for a Chopped Pyrgeometer
96 JOURNAL OF ATMOSPHERIC AND OCEANIC TECHNOLOGY VOLUME 17 An Imroved Calibration Method for a Choed Pyrgeometer FRIEDRICH FERGG OtoLab, Ingenieurbüro, Munich, Germany PETER WENDLING Deutsches Forschungszentrum
More informationTools and Algorithms in Bioinformatics
Tools and Algorithms in Bioinformatics GCBA815, Fall 2015 Week-4 BLAST Algorithm Continued Multiple Sequence Alignment Babu Guda, Ph.D. Department of Genetics, Cell Biology & Anatomy Bioinformatics and
More informationConvex Optimization methods for Computing Channel Capacity
Convex Otimization methods for Comuting Channel Caacity Abhishek Sinha Laboratory for Information and Decision Systems (LIDS), MIT sinhaa@mit.edu May 15, 2014 We consider a classical comutational roblem
More informationDeriving Indicator Direct and Cross Variograms from a Normal Scores Variogram Model (bigaus-full) David F. Machuca Mory and Clayton V.
Deriving ndicator Direct and Cross Variograms from a Normal Scores Variogram Model (bigaus-full) David F. Machuca Mory and Clayton V. Deutsch Centre for Comutational Geostatistics Deartment of Civil &
More informationFinite Mixture EFA in Mplus
Finite Mixture EFA in Mlus November 16, 2007 In this document we describe the Mixture EFA model estimated in Mlus. Four tyes of deendent variables are ossible in this model: normally distributed, ordered
More informationMoreover, the circular logic
Moreover, the circular logic How do we know what is the right distance without a good alignment? And how do we construct a good alignment without knowing what substitutions were made previously? ATGCGT--GCAAGT
More informationAlgorithms in Bioinformatics FOUR Pairwise Sequence Alignment. Pairwise Sequence Alignment. Convention: DNA Sequences 5. Sequence Alignment
Algorithms in Bioinformatics FOUR Sami Khuri Department of Computer Science San José State University Pairwise Sequence Alignment Homology Similarity Global string alignment Local string alignment Dot
More informationPhysicochemical properties of GPCR amino acid sequences for understanding GPCR-G-protein coupling
Chem-Bio Informatics Journal, Vol. 8, No. 2,.49-57 (2008) Physicochemical roerties of GPCR amino acid sequences for understanding GPCR-G-rotein couling Ganga D. Ghimire 1, 2*, Hideki Tanizawa 2, Masashi
More informationPhylogenetic Analysis. Han Liang, Ph.D. Assistant Professor of Bioinformatics and Computational Biology UT MD Anderson Cancer Center
Phylogenetic Analysis Han Liang, Ph.D. Assistant Professor of Bioinformatics and Computational Biology UT MD Anderson Cancer Center Outline Basic Concepts Tree Construction Methods Distance-based methods
More informationDistributed Rule-Based Inference in the Presence of Redundant Information
istribution Statement : roved for ublic release; distribution is unlimited. istributed Rule-ased Inference in the Presence of Redundant Information June 8, 004 William J. Farrell III Lockheed Martin dvanced
More informationPretest (Optional) Use as an additional pacing tool to guide instruction. August 21
Trimester 1 Pretest (Otional) Use as an additional acing tool to guide instruction. August 21 Beyond the Basic Facts In Trimester 1, Grade 7 focus on multilication. Daily Unit 1: The Number System Part
More information5. PRESSURE AND VELOCITY SPRING Each component of momentum satisfies its own scalar-transport equation. For one cell:
5. PRESSURE AND VELOCITY SPRING 2019 5.1 The momentum equation 5.2 Pressure-velocity couling 5.3 Pressure-correction methods Summary References Examles 5.1 The Momentum Equation Each comonent of momentum
More informationPhylogenetic trees 07/10/13
Phylogenetic trees 07/10/13 A tree is the only figure to occur in On the Origin of Species by Charles Darwin. It is a graphical representation of the evolutionary relationships among entities that share
More informationEvolutionary Tree Analysis. Overview
CSI/BINF 5330 Evolutionary Tree Analysis Young-Rae Cho Associate Professor Department of Computer Science Baylor University Overview Backgrounds Distance-Based Evolutionary Tree Reconstruction Character-Based
More informationMultiple Sequence Alignment, Gunnar Klau, December 9, 2005, 17:
Multiple Sequence Alignment, Gunnar Klau, December 9, 2005, 17:50 5001 5 Multiple Sequence Alignment The first part of this exposition is based on the following sources, which are recommended reading:
More informationChapter 6. Thermodynamics and the Equations of Motion
Chater 6 hermodynamics and the Equations of Motion 6.1 he first law of thermodynamics for a fluid and the equation of state. We noted in chater 4 that the full formulation of the equations of motion required
More informationDETC2003/DAC AN EFFICIENT ALGORITHM FOR CONSTRUCTING OPTIMAL DESIGN OF COMPUTER EXPERIMENTS
Proceedings of DETC 03 ASME 003 Design Engineering Technical Conferences and Comuters and Information in Engineering Conference Chicago, Illinois USA, Setember -6, 003 DETC003/DAC-48760 AN EFFICIENT ALGORITHM
More informationPulse Propagation in Optical Fibers using the Moment Method
Pulse Proagation in Otical Fibers using the Moment Method Bruno Miguel Viçoso Gonçalves das Mercês, Instituto Suerior Técnico Abstract The scoe of this aer is to use the semianalytic technique of the Moment
More informationComputational Biology
Computational Biology Lecture 6 31 October 2004 1 Overview Scoring matrices (Thanks to Shannon McWeeney) BLAST algorithm Start sequence alignment 2 1 What is a homologous sequence? A homologous sequence,
More information9/30/11. Evolution theory. Phylogenetic Tree Reconstruction. Phylogenetic trees (binary trees) Phylogeny (phylogenetic tree)
I9 Introduction to Bioinformatics, 0 Phylogenetic ree Reconstruction Yuzhen Ye (yye@indiana.edu) School of Informatics & omputing, IUB Evolution theory Speciation Evolution of new organisms is driven by
More informationAmira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut
Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut University-Egypt Phylogenetic analysis Phylogenetic Basics: Biological
More informationSara C. Madeira. Universidade da Beira Interior. (Thanks to Ana Teresa Freitas, IST for useful resources on this subject)
Bioinformática Sequence Alignment Pairwise Sequence Alignment Universidade da Beira Interior (Thanks to Ana Teresa Freitas, IST for useful resources on this subject) 1 16/3/29 & 23/3/29 27/4/29 Outline
More informationInDel 3-5. InDel 8-9. InDel 3-5. InDel 8-9. InDel InDel 8-9
Lecture 5 Alignment I. Introduction. For sequence data, the process of generating an alignment establishes positional homologies; that is, alignment provides the identification of homologous phylogenetic
More informationCryptanalysis of Pseudorandom Generators
CSE 206A: Lattice Algorithms and Alications Fall 2017 Crytanalysis of Pseudorandom Generators Instructor: Daniele Micciancio UCSD CSE As a motivating alication for the study of lattice in crytograhy we
More informationOne-way ANOVA Inference for one-way ANOVA
One-way ANOVA Inference for one-way ANOVA IPS Chater 12.1 2009 W.H. Freeman and Comany Objectives (IPS Chater 12.1) Inference for one-way ANOVA Comaring means The two-samle t statistic An overview of ANOVA
More information1. INTRODUCTION. Fn 2 = F j F j+1 (1.1)
CERTAIN CLASSES OF FINITE SUMS THAT INVOLVE GENERALIZED FIBONACCI AND LUCAS NUMBERS The beautiful identity R.S. Melham Deartment of Mathematical Sciences, University of Technology, Sydney PO Box 23, Broadway,
More informationUnit 1 - Computer Arithmetic
FIXD-POINT (FX) ARITHMTIC Unit 1 - Comuter Arithmetic INTGR NUMBRS n bit number: b n 1 b n 2 b 0 Decimal Value Range of values UNSIGND n 1 SIGND D = b i 2 i D = 2 n 1 b n 1 + b i 2 i n 2 i=0 i=0 [0, 2
More informationROC n Rule Learning - Towards a Better Understanding of Covering Algorithms
ROC n Rule Learning - Towards a Better Understanding of Covering Algorithms Johannes Fürnkranz (juffi@oefai.at) Austrian Research Institute for Artificial Intelligence, Schottengasse 3, A-1010 Wien, Austria
More informationA New GP-evolved Formulation for the Relative Permittivity of Water and Steam
ew GP-evolved Formulation for the Relative Permittivity of Water and Steam S. V. Fogelson and W. D. Potter rtificial Intelligence Center he University of Georgia, US Contact Email ddress: sergeyf1@uga.edu
More informationDr. Shalabh Department of Mathematics and Statistics Indian Institute of Technology Kanpur
Analysis of Variance and Design of Exeriment-I MODULE II LECTURE -4 GENERAL LINEAR HPOTHESIS AND ANALSIS OF VARIANCE Dr. Shalabh Deartment of Mathematics and Statistics Indian Institute of Technology Kanur
More informationConstructing Evolutionary/Phylogenetic Trees
Constructing Evolutionary/Phylogenetic Trees 2 broad categories: istance-based methods Ultrametric Additive: UPGMA Transformed istance Neighbor-Joining Character-based Maximum Parsimony Maximum Likelihood
More informationLecture 5,6 Local sequence alignment
Lecture 5,6 Local sequence alignment Chapter 6 in Jones and Pevzner Fall 2018 September 4,6, 2018 Evolution as a tool for biological insight Nothing in biology makes sense except in the light of evolution
More informationState Estimation with ARMarkov Models
Deartment of Mechanical and Aerosace Engineering Technical Reort No. 3046, October 1998. Princeton University, Princeton, NJ. State Estimation with ARMarkov Models Ryoung K. Lim 1 Columbia University,
More informationWeek 5: Distance methods, DNA and protein models
Week 5: Distance methods, DNA and protein models Genome 570 February, 2016 Week 5: Distance methods, DNA and protein models p.1/69 A tree and the expected distances it predicts E A 0.08 0.05 0.06 0.03
More informationPretest (Optional) Use as an additional pacing tool to guide instruction. August 21
Trimester 1 Pretest (Otional) Use as an additional acing tool to guide instruction. August 21 Beyond the Basic Facts In Trimester 1, Grade 8 focus on multilication. Daily Unit 1: Rational vs. Irrational
More informationq-ary Symmetric Channel for Large q
List-Message Passing Achieves Caacity on the q-ary Symmetric Channel for Large q Fan Zhang and Henry D Pfister Deartment of Electrical and Comuter Engineering, Texas A&M University {fanzhang,hfister}@tamuedu
More informationUse of Transformations and the Repeated Statement in PROC GLM in SAS Ed Stanek
Use of Transformations and the Reeated Statement in PROC GLM in SAS Ed Stanek Introduction We describe how the Reeated Statement in PROC GLM in SAS transforms the data to rovide tests of hyotheses of interest.
More informationCombining Logistic Regression with Kriging for Mapping the Risk of Occurrence of Unexploded Ordnance (UXO)
Combining Logistic Regression with Kriging for Maing the Risk of Occurrence of Unexloded Ordnance (UXO) H. Saito (), P. Goovaerts (), S. A. McKenna (2) Environmental and Water Resources Engineering, Deartment
More informationMultiple Sequence Alignment: HMMs and Other Approaches
Multiple Sequence Alignment: HMMs and Other Approaches Background Readings: Durbin et. al. Section 3.1, Ewens and Grant, Ch4. Wing-Kin Sung, Ch 6 Beerenwinkel N, Siebourg J. Statistics, probability, and
More informationRobust Predictive Control of Input Constraints and Interference Suppression for Semi-Trailer System
Vol.7, No.7 (4),.37-38 htt://dx.doi.org/.457/ica.4.7.7.3 Robust Predictive Control of Inut Constraints and Interference Suression for Semi-Trailer System Zhao, Yang Electronic and Information Technology
More informationTopic: Lower Bounds on Randomized Algorithms Date: September 22, 2004 Scribe: Srinath Sridhar
15-859(M): Randomized Algorithms Lecturer: Anuam Guta Toic: Lower Bounds on Randomized Algorithms Date: Setember 22, 2004 Scribe: Srinath Sridhar 4.1 Introduction In this lecture, we will first consider
More informationMath 239: Discrete Mathematics for the Life Sciences Spring Lecture 14 March 11. Scribe/ Editor: Maria Angelica Cueto/ C.E.
Math 239: Discrete Mathematics for the Life Sciences Spring 2008 Lecture 14 March 11 Lecturer: Lior Pachter Scribe/ Editor: Maria Angelica Cueto/ C.E. Csar 14.1 Introduction The goal of today s lecture
More informationBayesian Model Averaging Kriging Jize Zhang and Alexandros Taflanidis
HIPAD LAB: HIGH PERFORMANCE SYSTEMS LABORATORY DEPARTMENT OF CIVIL AND ENVIRONMENTAL ENGINEERING AND EARTH SCIENCES Bayesian Model Averaging Kriging Jize Zhang and Alexandros Taflanidis Why use metamodeling
More informationNamed Entity Recognition using Maximum Entropy Model SEEM5680
Named Entity Recognition using Maximum Entroy Model SEEM5680 Named Entity Recognition System Named Entity Recognition (NER): Identifying certain hrases/word sequences in a free text. Generally it involves
More informationFactors Effect on the Saturation Parameter S and there Influences on the Gain Behavior of Ytterbium Doped Fiber Amplifier
Australian Journal of Basic and Alied Sciences, 5(12): 2010-2020, 2011 ISSN 1991-8178 Factors Effect on the Saturation Parameter S and there Influences on the Gain Behavior of Ytterbium Doed Fiber Amlifier
More informationApproximating min-max k-clustering
Aroximating min-max k-clustering Asaf Levin July 24, 2007 Abstract We consider the roblems of set artitioning into k clusters with minimum total cost and minimum of the maximum cost of a cluster. The cost
More informationCSCI1950 Z Computa4onal Methods for Biology Lecture 4. Ben Raphael February 2, hhp://cs.brown.edu/courses/csci1950 z/ Algorithm Summary
CSCI1950 Z Computa4onal Methods for Biology Lecture 4 Ben Raphael February 2, 2009 hhp://cs.brown.edu/courses/csci1950 z/ Algorithm Summary Parsimony Probabilis4c Method Input Output Sankoff s & Fitch
More informationOn Line Parameter Estimation of Electric Systems using the Bacterial Foraging Algorithm
On Line Parameter Estimation of Electric Systems using the Bacterial Foraging Algorithm Gabriel Noriega, José Restreo, Víctor Guzmán, Maribel Giménez and José Aller Universidad Simón Bolívar Valle de Sartenejas,
More informationUsing algebraic geometry for phylogenetic reconstruction
Using algebraic geometry for phylogenetic reconstruction Marta Casanellas i Rius (joint work with Jesús Fernández-Sánchez) Departament de Matemàtica Aplicada I Universitat Politècnica de Catalunya IMA
More informationClassical gas (molecules) Phonon gas Number fixed Population depends on frequency of mode and temperature: 1. For each particle. For an N-particle gas
Lecture 14: Thermal conductivity Review: honons as articles In chater 5, we have been considering quantized waves in solids to be articles and this becomes very imortant when we discuss thermal conductivity.
More informationLecture 4: Evolutionary models and substitution matrices (PAM and BLOSUM).
1 Bioinformatics: In-depth PROBABILITY & STATISTICS Spring Semester 2011 University of Zürich and ETH Zürich Lecture 4: Evolutionary models and substitution matrices (PAM and BLOSUM). Dr. Stefanie Muff
More informationDr. Amira A. AL-Hosary
Phylogenetic analysis Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut University-Egypt Phylogenetic Basics: Biological
More informationGeneral Linear Model Introduction, Classes of Linear models and Estimation
Stat 740 General Linear Model Introduction, Classes of Linear models and Estimation An aim of scientific enquiry: To describe or to discover relationshis among events (variables) in the controlled (laboratory)
More informationChapter 7 Rational and Irrational Numbers
Chater 7 Rational and Irrational Numbers In this chater we first review the real line model for numbers, as discussed in Chater 2 of seventh grade, by recalling how the integers and then the rational numbers
More informationUsing Factor Analysis to Study the Effecting Factor on Traffic Accidents
Using Factor Analysis to Study the Effecting Factor on Traffic Accidents Abstract Layla A. Ahmed Deartment of Mathematics, College of Education, University of Garmian, Kurdistan Region Iraq This aer is
More informationKeywords: pile, liquefaction, lateral spreading, analysis ABSTRACT
Key arameters in seudo-static analysis of iles in liquefying sand Misko Cubrinovski Deartment of Civil Engineering, University of Canterbury, Christchurch 814, New Zealand Keywords: ile, liquefaction,
More informationLecture Notes: Markov chains
Computational Genomics and Molecular Biology, Fall 5 Lecture Notes: Markov chains Dannie Durand At the beginning of the semester, we introduced two simple scoring functions for pairwise alignments: a similarity
More informationMaximum Cardinality Matchings on Trees by Randomized Local Search
Maximum Cardinality Matchings on Trees by Randomized Local Search ABSTRACT Oliver Giel Fachbereich Informatik, Lehrstuhl 2 Universität Dortmund 44221 Dortmund, Germany oliver.giel@cs.uni-dortmund.de To
More information