Multiple Alignment. Slides revised and adapted to Bioinformática IST Ana Teresa Freitas
|
|
- Ralph Miller
- 5 years ago
- Views:
Transcription
1 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 in 3-D Progressive lignment Profile Progressive lignment (lustalw) Scoring Multiple lignments Entropy Sum of Pairs lignment
2 n Introduction to Bioinformatics lgorithms eneralizing the Notion of Pairwise lignment Up until now we have only tried to align two sequences to one another. What about more than two? lignment of 2 sequences is represented as a 2-row matrix In a similar way, we represent alignment of 3 sequences as a 3-row matrix _ Score: more conserved columns, better alignment n Introduction to Bioinformatics lgorithms lignments = Paths in lign 3 sequences:,,
3 n Introduction to Bioinformatics lgorithms lignment Paths x coordinate n Introduction to Bioinformatics lgorithms lignment Paths lign the following 3 sequences:,, x coordinate y coordinate -- 3
4 n Introduction to Bioinformatics lgorithms lignment Paths x coordinate y coordinate z coordinate Resulting path in (x,y,z) space: (0,0,0) (,,0) (,2,) (2,3,2) (3,3,3) (4,4,4) n Introduction to Bioinformatics lgorithms ligning hree Sequences Same strategy as aligning two sequences Use a 3-D Manhattan ube, with each axis representing a sequence to align For global alignments, go from source to sink source sink 4
5 n Introduction to Bioinformatics lgorithms 2-D vs 3-D lignment rid V W 2-D edit graph 3-D? n Introduction to Bioinformatics lgorithms rchitecture of 3-D lignment rid In 2-D, 3 edges in each unit square In 3-D, 7 edges in each unit cube 5
6 n Introduction to Bioinformatics lgorithms ell of 3-D lignment rid (i-,j-,k-) (i-,j,k-) (i-,j-,k) (i-,j,k) (i,j-,k-) (i,j,k-) (i,j-,k) (i,j,k) n Introduction to Bioinformatics lgorithms Multiple lignment: Dynamic Programming s i,j,k = max s i-,j-,k- + σ(v i, w j, u k ) s i-,j-,k + σ(v i, w j, _ ) s i-,j,k- + σ(v i, _, u k ) s i,j-,k- + σ(_, w j, u k ) s i-,j,k + σ(v i, _, _) s i,j-,k + σ(_, w j, _) s i,j,k- + σ(_, _, u k ) cube diagonal: no indels face diagonal: one indel edge diagonal: two indels σ(x, y, z) is an entry in the 3-D scoring matrix 6
7 n Introduction to Bioinformatics lgorithms Multiple lignment: Running ime 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 ) onclusion: dynamic programming approach for alignment between two sequences is easily extended to k sequences but it is impractical due to exponential running time n Introduction to Bioinformatics lgorithms Inferring Multiple lignment from Pairwise lignments From an optimal multiple alignment, we can infer pairwise alignments between all sequences, but they are not necessarily optimal It is difficult to infer a ``good multiple alignment from optimal pairwise alignments between all sequences 7
8 n Introduction to Bioinformatics lgorithms ombining Optimal Pairwise lignments into Multiple lignment an combine pairwise alignments into multiple alignment an not combine pairwise alignments into multiple alignment n Introduction to Bioinformatics lgorithms Inferring Pairwise lignments 3 sequences, 3 comparisons 4 sequences, 6 comparisons 5 sequences, 0 comparisons 8
9 n Introduction to Bioinformatics lgorithms Multiple lignment: reedy pproach hoose most similar pair of strings and combine into a consensus, thereby reducing alignment of k sequences to an alignment of of k- sequences. Repeat his is a heuristic greedy method k u = u 2 = u 3 = u = --- u 2 = u k = k- u k = n Introduction to Bioinformatics lgorithms reedy pproach: Example onsider these 4 sequences s s2 s3 s4 9
10 n Introduction to Bioinformatics lgorithms reedy pproach: Example (cont d) here are 4 2 = 6 possible alignments s2 s4 (score = 2) s - s2 - (score = ) s - s3 - (score = ) s -- s4 - (score = 0) s2 - s3 - (score = -) s3 - s4 - (score = -) n Introduction to Bioinformatics lgorithms reedy pproach: Example (cont d) s2 and s4 are closest; combine: s2 s4 s s3 s2,4 s2,4 (consensus) here are many (4) alternative choices for the consensus, let s assume we randomly choose one new set becomes: 0
11 n Introduction to Bioinformatics lgorithms reedy pproach: Example (cont d) set is: s s3 s2,4 scores are: s - s3 - (score = ) s -- s2,4 -- (score = 0) s3 s2,4 - (score=-) ake best pair and form another consensus: s,3 = (arbitrarily break ties) n Introduction to Bioinformatics lgorithms reedy pproach: Example (cont d) new set is: s,3 s2,4 scores is: s,3 s2,4 - (score=-) Form consensus: s,3,2,4 = (arbitrarily break ties) s s2 s3 s4
12 n Introduction to Bioinformatics lgorithms Progressive lignment Progressive alignment is a variation of greedy algorithm with a somewhat more intelligent strategy for choosing a consensus Progressive alignment works well for close sequences, but deteriorates for distant sequences aps in consensus string are permanent Simplified representation of the alignments Better solution? Use a profile to represent consensus n Introduction to Bioinformatics lgorithms lustalw Popular multiple alignment tool today Several heuristics to improve accuracy: Sequences are weighted by relatedness Scoring matrix can be chosen on the fly Position-specific gap penalties 2
13 n Introduction to Bioinformatics lgorithms lustalw (cont d) hree-step process.) Pairwise alignment 2.) Build uide ree 3.) Progressive lignment n Introduction to Bioinformatics lgorithms Step : Pairwise lignment ligns each sequence again each other giving a distance matrix Distance = exact matches / sequence length (percent identity) S S 2 S 3 S 4 S S S S (.7 means 7 % identical) 3
14 n Introduction to Bioinformatics lgorithms Step 2: uide ree reate uide ree using the distance matrix lustalw uses the neighbor-joining method uide tree roughly reflects evolutionary relations n Introduction to Bioinformatics lgorithms Step 2: uide ree (cont d) S S 2 S 3 S 4 S S S S S S 3 S 4 S 2 alculate: s,3 = consensus(s, s3) s,3,4 = consensus((s,3),s4) s,3,4,2,2 = consensus((s,3,4),s2) 4
15 n Introduction to Bioinformatics lgorithms Step 3: Progressive lignment lign the two most similar sequences Following the guide tree, add in the next sequences, aligning to the existing alignment Insert gaps as necessary Sample output: FOS_R FOS_MOUSE FOS_HIK FOSB_MOUSE FOSB_HUMN PEEMSVS-LDLLPEPESEEFLPLLNDPEPK-PSLEPVKNISNMELKEPFD PEEMSVS-LDLLPESPESEEFLPLLNDPEPK-PSLEPVKSISNVELKEPFD SEELLDL----PSPEEFLPLMEPPVPPKEPS--SLELKEPFD PPPLEVRDLP-----SSKEDFWLLPPPPPPP LPFQ PPPLEVRDLP-----SPKEDFSWLLPPPPPPP LPFQ.. : **. :.. *:.* *. * **: Dots and stars show how well-conserved a column is. n Introduction to Bioinformatics lgorithms lustalw: Scoring lignments Distance between sequences determines which scoring matrix to use 80-00% Blosum % Blosum % Blosum % Blosum30 5
16 n Introduction to Bioinformatics lgorithms Multiple lignments: Scoring Number of matches (multiple longest common subsequence score) Entropy score Sum of pairs (SP-Score) n Introduction to Bioinformatics lgorithms Multiple LS Score column is a match if all the letters in the column are the same Only good for very similar sequences 6
17 n Introduction to Bioinformatics lgorithms Entropy Define frequencies for the occurrence of each letter in each column of multiple alignment p = or p = 0.75, p = 0.25 ompute entropy of each column X p X =,,, log p X n Introduction to Bioinformatics lgorithms Entropy: Example entropy = 0 Best case Worst case entropy = log 4 4 = 4( 2) = 2 4 7
18 n Introduction to Bioinformatics lgorithms Multiple lignment: Entropy Score Entropy for a multiple alignment is the sum of entropies of its columns: Σ over all columns Σ X=,,, p X logp X n Introduction to Bioinformatics lgorithms Entropy of an lignment: Example column entropy: ( p logp + p logp + p logp + p logp ) olumn = [*log() + 0*log0 + 0*log0 +0*log0] = 0 olumn 2 = [( / 4 )*log( / 4 ) + ( 3 / 4 )*log( 3 / 4 ) + 0*log0 + 0*log0] = [ ( / 4 )*(-2) + ( 3 / 4 )*(-.45) ] = -0.8 olumn 3 = [( / 4 )*log( / 4 )+( / 4 )*log( / 4 )+( / 4 )*log( / 4 ) +( / 4 )*log( / 4 )] = 4* -[( / 4 )*(-2)] = -2 lignment Entropy = =
19 n Introduction to Bioinformatics lgorithms Inferring Pairwise lignments from Multiple lignments From a multiple alignment, we can infer pairwise alignments between all sequences, but they are not necessarily optimal his is like projecting a 3-D multiple alignment path on to a 2-D face of the cube n Introduction to Bioinformatics lgorithms Multiple lignment Projections 3-D alignment can be projected onto the 2-D plane to represent an alignment between a pair of sequences. ll 3 Pairwise Projections of the Multiple lignment 9
20 n Introduction to Bioinformatics lgorithms Sum of Pairs Score(SP-Score) onsider pairwise alignment of sequences a i and a j imposed by a multiple alignment of k sequences Denote the score of this suboptimal (not necessarily optimal) pairwise alignment as s*(a i, a j ) Sum up the pairwise scores for a multiple alignment: s(a,,a k ) = Σ i,j s*(a i, a j ) n Introduction to Bioinformatics lgorithms omputing SP-Score ligning 4 sequences: 6 pairwise alignments iven a,a 2,a 3,a 4 : s(a a 4 ) = Σs*(a i,a j ) = s*(a,a 2 ) + s*(a,a 3 ) + s*(a,a 4 ) + s*(a 2,a 3 ) + s*(a 2,a 4 ) + s*(a 3,a 4 ) 20
21 n Introduction to Bioinformatics lgorithms SP-Score: Example s. s k = o calculate each column: ss ( a s * ( *... ak ) S ( ai, a j ) i, j n Pairs of Sequences 2 = 3 µ Score = 2µ µ olumn olumn 3 2
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
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 sequences
More informationBackground: comparative genomics. Sequence similarity. Homologs. Similarity vs homology (2) Similarity vs homology. Sequence Alignment (chapter 6)
Sequence lignment (chapter ) he biological problem lobal alignment Local alignment Multiple alignment Background: comparative genomics Basic question in biology: what properties are shared among organisms?
More informationSequence Alignment (chapter 6)
Sequence lignment (chapter 6) he biological problem lobal alignment Local alignment Multiple alignment Introduction to bioinformatics, utumn 6 Background: comparative genomics Basic question in biology:
More informationp(-,i)+p(,i)+p(-,v)+p(i,v),v)+p(i,v)
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
More informationAlgorithms in Bioinformatics
Algorithms in Bioinformatics Sami Khuri Department of omputer Science San José State University San José, alifornia, USA khuri@cs.sjsu.edu www.cs.sjsu.edu/faculty/khuri Pairwise Sequence Alignment Homology
More informationMultiple Sequence Alignment
Multiple equence lignment Four ami Khuri Dept of omputer cience an José tate University Multiple equence lignment v Progressive lignment v Guide Tree v lustalw v Toffee v Muscle v MFFT * 20 * 0 * 60 *
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 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 informationPairwise & Multiple sequence alignments
Pairwise & Multiple sequence alignments Urmila Kulkarni-Kale Bioinformatics Centre 411 007 urmila@bioinfo.ernet.in Basis for Sequence comparison Theory of evolution: gene sequences have evolved/derived
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 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 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 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 informationMultiple Sequence Alignment (MAS)
Multiple Sequence lignment (MS) Group-to-group alignments Steven driaensen & Ken Tanaka References Osamu Goto Optimal lignment between groups of sequences and its application to multiple sequence alignment
More informationBioinformatics for Computer Scientists (Part 2 Sequence Alignment) Sepp Hochreiter
Bioinformatics for Computer Scientists (Part 2 Sequence Alignment) Institute of Bioinformatics Johannes Kepler University, Linz, Austria Sequence Alignment 2. Sequence Alignment Sequence Alignment 2.1
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 informationPage 1. Evolutionary Trees. Why build evolutionary tree? Outline
Page Evolutionary Trees Russ. ltman MI S 7 Outline. Why build evolutionary trees?. istance-based vs. character-based methods. istance-based: Ultrametric Trees dditive Trees. haracter-based: Perfect phylogeny
More informationA graph kernel approach to the identification and characterisation of structured non-coding RNAs using multiple sequence alignment information
graph kernel approach to the identification and characterisation of structured noncoding RNs using multiple sequence alignment information Mariam lshaikh lbert Ludwigs niversity Freiburg, Department of
More informationSequence Bioinformatics. Multiple Sequence Alignment Waqas Nasir
Sequence Bioinformatics Multiple Sequence Alignment Waqas Nasir 2010-11-12 Multiple Sequence Alignment One amino acid plays coy; a pair of homologous sequences whisper; many aligned sequences shout out
More informationSequence Alignment: A General Overview. COMP Fall 2010 Luay Nakhleh, Rice University
Sequence Alignment: A General Overview COMP 571 - Fall 2010 Luay Nakhleh, Rice University Life through Evolution All living organisms are related to each other through evolution This means: any pair of
More informationPAM-1 Matrix 10,000. From: Ala Arg Asn Asp Cys Gln Glu To:
119-1 atrix 10,000 rom: la rg sn sp ys ln lu o: la 9867 2 9 10 3 8 17 rg 1 9913 1 0 1 10 0 sn 4 1 9822 36 0 4 6 sp 6 0 42 9859 0 6 53 ys 1 1 0 0 9973 0 0 ln 3 9 4 5 0 9876 27 lu 10 0 7 56 0 35 9865 120
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 informationDynamic Programming: Edit Distance
Dynamic Programming: Edit Distance Bioinformatics: Issues and Algorithms SE 308-408 Fall 2007 Lecture 10 Lopresti Fall 2007 Lecture 10-1 - Outline Setting the Stage DNA Sequence omparison: First Successes
More informationIn-Depth Assessment of Local Sequence Alignment
2012 International Conference on Environment Science and Engieering IPCBEE vol.3 2(2012) (2012)IACSIT Press, Singapoore In-Depth Assessment of Local Sequence Alignment Atoosa Ghahremani and Mahmood A.
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 informationConserved RNA Structures. Ivo L. Hofacker. Institut for Theoretical Chemistry, University Vienna.
onserved RN Structures Ivo L. Hofacker Institut for Theoretical hemistry, University Vienna http://www.tbi.univie.ac.at/~ivo/ Bled, January 2002 Energy Directed Folding Predict structures from sequence
More informationPhylogeny Tree Algorithms
Phylogeny Tree lgorithms Jianlin heng, PhD School of Electrical Engineering and omputer Science University of entral Florida 2006 Free for academic use. opyright @ Jianlin heng & original sources for some
More informationIntroduction to Bioinformatics Algorithms Homework 3 Solution
Introduction to Bioinformatics Algorithms Homework 3 Solution Saad Mneimneh Computer Science Hunter College of CUNY Problem 1: Concave penalty function We have seen in class the following recurrence for
More informationSequence analysis and comparison
The aim with sequence identification: Sequence analysis and comparison Marjolein Thunnissen Lund September 2012 Is there any known protein sequence that is homologous to mine? Are there any other species
More informationChapter 6. Weighted Interval Scheduling. Dynamic Programming. Algorithmic Paradigms. Dynamic Programming Applications
lgorithmic Paradigms hapter Dynamic Programming reedy. Build up a solution incrementally, myopically optimizing some local criterion. Divide-and-conquer. Break up a problem into sub-problems, solve each
More informationDynamic Programming. Weighted Interval Scheduling. Algorithmic Paradigms. Dynamic Programming
lgorithmic Paradigms Dynamic Programming reed Build up a solution incrementally, myopically optimizing some local criterion Divide-and-conquer Break up a problem into two sub-problems, solve each sub-problem
More informationBioinformatics (GLOBEX, Summer 2015) Pairwise sequence alignment
Bioinformatics (GLOBEX, Summer 2015) Pairwise sequence alignment Substitution score matrices, PAM, BLOSUM Needleman-Wunsch algorithm (Global) Smith-Waterman algorithm (Local) BLAST (local, heuristic) E-value
More informationSequence Alignments. Dynamic programming approaches, scoring, and significance. Lucy Skrabanek ICB, WMC January 31, 2013
Sequence Alignments Dynamic programming approaches, scoring, and significance Lucy Skrabanek ICB, WMC January 31, 213 Sequence alignment Compare two (or more) sequences to: Find regions of conservation
More informationTandem Mass Spectrometry: Generating function, alignment and assembly
Tandem Mass Spectrometry: Generating function, alignment and assembly With slides from Sangtae Kim and from Jones & Pevzner 2004 Determining reliability of identifications Can we use Target/Decoy to estimate
More informationIntroduction to Bioinformatics
Introduction to Bioinformatics Lecture : p he biological problem p lobal alignment p Local alignment p Multiple alignment 6 Background: comparative genomics p Basic question in biology: what properties
More informationHidden Markov Models
Hidden Markov Models Slides revised and adapted to Bioinformática 55 Engª Biomédica/IST 2005 Ana Teresa Freitas Forward Algorithm For Markov chains we calculate the probability of a sequence, P(x) How
More informationSequence analysis and Genomics
Sequence analysis and Genomics October 12 th November 23 rd 2 PM 5 PM Prof. Peter Stadler Dr. Katja Nowick Katja: group leader TFome and Transcriptome Evolution Bioinformatics group Paul-Flechsig-Institute
More informationSequence comparison: Score matrices
Sequence comparison: Score matrices http://facultywashingtonedu/jht/gs559_2013/ Genome 559: Introduction to Statistical and omputational Genomics Prof James H Thomas FYI - informal inductive proof of best
More informationEECS730: Introduction to Bioinformatics
EECS730: Introduction to Bioinformatics Lecture 03: Edit distance and sequence alignment Slides adapted from Dr. Shaojie Zhang (University of Central Florida) KUMC visit How many of you would like to attend
More informationSequence comparison: Score matrices. Genome 559: Introduction to Statistical and Computational Genomics Prof. James H. Thomas
Sequence comparison: Score matrices Genome 559: Introduction to Statistical and omputational Genomics Prof James H Thomas FYI - informal inductive proof of best alignment path onsider the last step in
More information3. SEQUENCE ANALYSIS BIOINFORMATICS COURSE MTAT
3. SEQUENCE ANALYSIS BIOINFORMATICS COURSE MTAT.03.239 25.09.2012 SEQUENCE ANALYSIS IS IMPORTANT FOR... Prediction of function Gene finding the process of identifying the regions of genomic DNA that encode
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 informationSequence comparison: Score matrices. Genome 559: Introduction to Statistical and Computational Genomics Prof. James H. Thomas
Sequence comparison: Score matrices Genome 559: Introduction to Statistical and omputational Genomics Prof James H Thomas Informal inductive proof of best alignment path onsider the last step in the best
More informationCISC 889 Bioinformatics (Spring 2004) Sequence pairwise alignment (I)
CISC 889 Bioinformatics (Spring 2004) Sequence pairwise alignment (I) Contents Alignment algorithms Needleman-Wunsch (global alignment) Smith-Waterman (local alignment) Heuristic algorithms FASTA BLAST
More informationPairwise Alignment. Guan-Shieng Huang. Dept. of CSIE, NCNU. Pairwise Alignment p.1/55
Pairwise Alignment Guan-Shieng Huang shieng@ncnu.edu.tw Dept. of CSIE, NCNU Pairwise Alignment p.1/55 Approach 1. Problem definition 2. Computational method (algorithms) 3. Complexity and performance Pairwise
More informationCFG PSA Algorithm. Sequence Alignment Guided By Common Motifs Described By Context Free Grammars
FG PS lgorithm Sequence lignment Guided By ommon Motifs Described By ontext Free Grammars motivation Find motifs- conserved regions that indicate a biological function or signature. Other algorithm do
More information17 Non-collinear alignment Motivation A B C A B C A B C A B C D A C. This exposition is based on:
17 Non-collinear alignment This exposition is based on: 1. Darling, A.E., Mau, B., Perna, N.T. (2010) progressivemauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5(6):e11147.
More informationCopyright 2000, Kevin Wayne 1
/9/ lgorithmic Paradigms hapter Dynamic Programming reed. Build up a solution incrementally, myopically optimizing some local criterion. Divide-and-conquer. Break up a problem into two sub-problems, solve
More informationComparing whole genomes
BioNumerics Tutorial: Comparing whole genomes 1 Aim The Chromosome Comparison window in BioNumerics has been designed for large-scale comparison of sequences of unlimited length. In this tutorial you will
More informationPhysics 212. Lecture 8. Today's Concept: Capacitors. Capacitors in a circuits, Dielectrics, Energy in capacitors. Physics 212 Lecture 8, Slide 1
Physics 212 Lecture 8 Today's oncept: apacitors apacitors in a circuits, Dielectrics, Energy in capacitors Physics 212 Lecture 8, Slide 1 Simple apacitor ircuit Q +Q -Q Q= Q Battery has moved charge Q
More information7.1 Sampling Error The Need for Sampling Distributions
7.1 Sampling Error The Need for Sampling Distributions Tom Lewis Fall Term 2009 Tom Lewis () 7.1 Sampling Error The Need for Sampling Distributions Fall Term 2009 1 / 5 Outline 1 Tom Lewis () 7.1 Sampling
More informationAreas. ! Bioinformatics. ! Control theory. ! Information theory. ! Operations research. ! Computer science: theory, graphics, AI, systems,.
lgorithmic Paradigms hapter Dynamic Programming reed Build up a solution incrementally, myopically optimizing some local criterion Divide-and-conquer Break up a problem into two sub-problems, solve each
More informationA Method for Aligning RNA Secondary Structures
Method for ligning RN Secondary Structures Jason T. L. Wang New Jersey Institute of Technology J Liu, JTL Wang, J Hu and B Tian, BM Bioinformatics, 2005 1 Outline Introduction Structural alignment of RN
More informationEECS730: Introduction to Bioinformatics
EECS730: Introduction to Bioinformatics Lecture 07: profile Hidden Markov Model http://bibiserv.techfak.uni-bielefeld.de/sadr2/databasesearch/hmmer/profilehmm.gif Slides adapted from Dr. Shaojie Zhang
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 informationNetwork alignment and querying
Network biology minicourse (part 4) Algorithmic challenges in genomics Network alignment and querying Roded Sharan School of Computer Science, Tel Aviv University Multiple Species PPI Data Rapid growth
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 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 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 informationDid you know that Multiple Alignment is NP-hard? Isaac Elias Royal Institute of Technology Sweden
Did you know that Multiple Alignment is NP-hard? Isaac Elias Royal Institute of Technology Sweden 1 Results Multiple Alignment with SP-score Star Alignment Tree Alignment (with given phylogeny) are NP-hard
More informationTools and Algorithms in Bioinformatics
Tools and Algorithms in Bioinformatics GCBA815, Fall 2013 Week3: Blast Algorithm, theory and practice Babu Guda, Ph.D. Department of Genetics, Cell Biology & Anatomy Bioinformatics and Systems Biology
More informationSequence Analysis '17 -- lecture 7
Sequence Analysis '17 -- lecture 7 Significance E-values How significant is that? Please give me a number for......how likely the data would not have been the result of chance,......as opposed to......a
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 informationBasics on bioinforma-cs Lecture 7. Nunzio D Agostino
Basics on bioinforma-cs Lecture 7 Nunzio D Agostino nunzio.dagostino@entecra.it; nunzio.dagostino@gmail.com Multiple alignments One sequence plays coy a pair of homologous sequence whisper many aligned
More informationCSE 549: Computational Biology. Substitution Matrices
CSE 9: Computational Biology Substitution Matrices How should we score alignments So far, we ve looked at arbitrary schemes for scoring mutations. How can we assign scores in a more meaningful way? Are
More informationEvolutionary Models. Evolutionary Models
Edit Operators In standard pairwise alignment, what are the allowed edit operators that transform one sequence into the other? Describe how each of these edit operations are represented on a sequence alignment
More informationLocal Alignment Statistics
Local Alignment Statistics Stephen Altschul National Center for Biotechnology Information National Library of Medicine National Institutes of Health Bethesda, MD Central Issues in Biological Sequence Comparison
More informationPairwise sequence alignment
Department of Evolutionary Biology Example Alignment between very similar human alpha- and beta globins: GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKL G+ +VK+HGKKV A+++++AH+D++ +++++LS+LH KL GNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKL
More informationGlobal alignments - review
Global alignments - review Take two sequences: X[j] and Y[j] M[i-1, j-1] ± 1 M[i, j] = max M[i, j-1] 2 M[i-1, j] 2 The best alignment for X[1 i] and Y[1 j] is called M[i, j] X[j] Initiation: M[,]= pply
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 informationLecture 2: Pairwise Alignment. CG Ron Shamir
Lecture 2: Pairwise Alignment 1 Main source 2 Why compare sequences? Human hexosaminidase A vs Mouse hexosaminidase A 3 www.mathworks.com/.../jan04/bio_genome.html Sequence Alignment עימוד רצפים The problem:
More informationStat 217 Final Exam. Name: May 1, 2002
Stat 217 Final Exam Name: May 1, 2002 Problem 1. Three brands of batteries are under study. It is suspected that the lives (in weeks) of the three brands are different. Five batteries of each brand are
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 informationPairwise sequence alignments
Pairwise sequence alignments Volker Flegel VI, October 2003 Page 1 Outline Introduction Definitions Biological context of pairwise alignments Computing of pairwise alignments Some programs VI, October
More informationBiochemistry 324 Bioinformatics. Pairwise sequence alignment
Biochemistry 324 Bioinformatics Pairwise sequence alignment How do we compare genes/proteins? When we have sequenced a genome, we try and identify the function of unknown genes by finding a similar gene
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 informationMULTIPLE SEQUENCE ALIGNMENT FOR CONSTRUCTION OF PHYLOGENETIC TREE
MULTIPLE SEQUENCE ALIGNMENT FOR CONSTRUCTION OF PHYLOGENETIC TREE Manmeet Kaur 1, Navneet Kaur Bawa 2 1 M-tech research scholar (CSE Dept) ACET, Manawala,Asr 2 Associate Professor (CSE Dept) ACET, Manawala,Asr
More informationAlgorithms in Bioinformatics
Algorithms in Bioinformatics Sami Khuri Department of Computer Science San José State University San José, California, USA khuri@cs.sjsu.edu www.cs.sjsu.edu/faculty/khuri RNA Structure Prediction Secondary
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 informationSA-REPC - Sequence Alignment with a Regular Expression Path Constraint
SA-REPC - Sequence Alignment with a Regular Expression Path Constraint Nimrod Milo Tamar Pinhas Michal Ziv-Ukelson Ben-Gurion University of the Negev, Be er Sheva, Israel Graduate Seminar, BGU 2010 Milo,
More informationCS100: DISCRETE STRUCTURES. Lecture 3 Matrices Ch 3 Pages:
CS100: DISCRETE STRUCTURES Lecture 3 Matrices Ch 3 Pages: 246-262 Matrices 2 Introduction DEFINITION 1: A matrix is a rectangular array of numbers. A matrix with m rows and n columns is called an m x n
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 informationBIO 285/CSCI 285/MATH 285 Bioinformatics Programming Lecture 8 Pairwise Sequence Alignment 2 And Python Function Instructor: Lei Qian Fisk University
BIO 285/CSCI 285/MATH 285 Bioinformatics Programming Lecture 8 Pairwise Sequence Alignment 2 And Python Function Instructor: Lei Qian Fisk University Measures of Sequence Similarity Alignment with dot
More informationThanks to Paul Lewis, Jeff Thorne, and Joe Felsenstein for the use of slides
hanks to Paul Lewis, Jeff horne, and Joe Felsenstein for the use of slides Hennigian logic reconstructs the tree if we know polarity of characters and there is no homoplasy UPM infers a tree from a distance
More informationOutline. Sequence-comparison methods. Buzzzzzzzz. Why compare sequences? Gerard Kleywegt Uppsala University
MB330 - January, 2006 Sequence-comparison methods erard Kleywegt Uppsala University Outline! Why compare sequences?! Dotplots! airwise sequence alignments &! Multiple sequence alignments! rofile methods!
More informationAn Introduction to Bioinformatics Algorithms Hidden Markov Models
Hidden Markov Models Outline 1. CG-Islands 2. The Fair Bet Casino 3. Hidden Markov Model 4. Decoding Algorithm 5. Forward-Backward Algorithm 6. Profile HMMs 7. HMM Parameter Estimation 8. Viterbi Training
More informationCountable and uncountable sets. Matrices.
CS 441 Discrete Mathematics for CS Lecture 11 Countable and uncountable sets. Matrices. Milos Hauskrecht milos@cs.pitt.edu 5329 Sennott Square Arithmetic series Definition: The sum of the terms of the
More informationSubstitution matrices
Introduction to Bioinformatics Substitution matrices Jacques van Helden Jacques.van-Helden@univ-amu.fr Université d Aix-Marseille, France Lab. Technological Advances for Genomics and Clinics (TAGC, INSERM
More informationBMI/CS 776 Lecture #20 Alignment of whole genomes. Colin Dewey (with slides adapted from those by Mark Craven)
BMI/CS 776 Lecture #20 Alignment of whole genomes Colin Dewey (with slides adapted from those by Mark Craven) 2007.03.29 1 Multiple whole genome alignment Input set of whole genome sequences genomes diverged
More informationSequence Alignment: Scoring Schemes. COMP 571 Luay Nakhleh, Rice University
Sequence Alignment: Scoring Schemes COMP 571 Luay Nakhleh, Rice University Scoring Schemes Recall that an alignment score is aimed at providing a scale to measure the degree of similarity (or difference)
More informationInteger Programming for Bayesian Network Structure Learning
Integer Programming for Bayesian Network Structure Learning James Cussens Helsinki, 2013-04-09 James Cussens IP for BNs Helsinki, 2013-04-09 1 / 20 Linear programming The Belgian diet problem Fat Sugar
More informationbioinformatics 1 -- lecture 7
bioinformatics 1 -- lecture 7 Probability and conditional probability Random sequences and significance (real sequences are not random) Erdos & Renyi: theoretical basis for the significance of an alignment
More informationPairwise sequence alignments. Vassilios Ioannidis (From Volker Flegel )
Pairwise sequence alignments Vassilios Ioannidis (From Volker Flegel ) Outline Introduction Definitions Biological context of pairwise alignments Computing of pairwise alignments Some programs Importance
More informationPair Hidden Markov Models
Pair Hidden Markov Models Scribe: Rishi Bedi Lecturer: Serafim Batzoglou January 29, 2015 1 Recap of HMMs alphabet: Σ = {b 1,...b M } set of states: Q = {1,..., K} transition probabilities: A = [a ij ]
More informationPhylogenetics Todd Vision Spring Some applications. Uncultured microbial diversity
Phylogenetics Todd Vision Spring 2008 Tree basics Sequence alignment Inferring a phylogeny Neighbor joining Maximum parsimony Maximum likelihood Rooting trees and measuring confidence Software and file
More informationApplication of Associative Matrices to Recognize DNA Sequences in Bioinformatics
Application of Associative Matrices to Recognize DNA Sequences in Bioinformatics 1. Introduction. Jorge L. Ortiz Department of Electrical and Computer Engineering College of Engineering University of Puerto
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 informationMatrix Basic Concepts
Matrix Basic Concepts Topics: What is a matrix? Matrix terminology Elements or entries Diagonal entries Address/location of entries Rows and columns Size of a matrix A column matrix; vectors Special types
More informationHidden Markov Models
Hidden Markov Models Outline 1. CG-Islands 2. The Fair Bet Casino 3. Hidden Markov Model 4. Decoding Algorithm 5. Forward-Backward Algorithm 6. Profile HMMs 7. HMM Parameter Estimation 8. Viterbi Training
More information