Pairwise Alignment. Guan-Shieng Huang. Dept. of CSIE, NCNU. Pairwise Alignment p.1/55
|
|
- Charlotte Ramsey
- 5 years ago
- Views:
Transcription
1 Pairwise Alignment Guan-Shieng Huang Dept. of CSIE, NCNU Pairwise Alignment p.1/55
2 Approach 1. Problem definition 2. Computational method (algorithms) 3. Complexity and performance Pairwise Alignment p.2/55
3 Motivations Reconstructing long sequences of DNA form overlapping sequence fragments Determining physical and genetic maps from probe data under various experiment protocols Database searching Pairwise Alignment p.3/55
4 Comparing two of more sequences for similarities Protein structure prediction (building profiles) Comparing the same gene sequenced by two different labs Pairwise Alignment p.4/55
5 Similarity & Difference 1. Common Ancestor Assumption 2. Mutation: (a) substitution (transition, transversion) (b) deletion (c) insertion We use indel to refer to deletion or insertion. Pairwise Alignment p.5/55
6 What is the difference between acctga and agcta? acctga agctga agct - a Pairwise Alignment p.6/55
7 Key Issues 1. notion of similarity/difference 2. the scoring system used to rank alignments 3. the algorithm used to find optimal scoring alignment 4. the statistical method used to evaluate the significance of an alignment score Pairwise Alignment p.7/55
8 Measure similarity by 1. substitution: 1 2. indel: 2 3. match: +1 Edit Distance a c c t g a a g c t - a = 1 Pairwise Alignment p.8/55
9 a c c t g a a - g c t a = 3 a c c t g a - a g c t a = 5 Pairwise Alignment p.9/55
10 x: x 1 x 2 x 3... x m y: y 1 y 2 y 3... y n Alphabet: Σ = {A, G, C, T } for DNA sequence Σ = {A, G, C, U} for RNA sequence Σ = {A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y } for proteins Pairwise Alignment p.10/55
11 s(a, b): the score to substitute a by b s(a, ): delete a s(, b): insert b Pairwise Alignment p.11/55
12 Nomenclature BIOLOGY COMPUTER SCIENCE - sequence - string, word - subsequence - substring (contiguous) - N/A - subsequence - N/A - exact matching - alignment - inexact matching Pairwise Alignment p.12/55
13 Algorithm for Pairwise Alignment To find the best alignment (with the highest score) through Brute-force Dynamic programming Pairwise Alignment p.13/55
14 Brute-force Algorithm Try all possible alignments of x and y. F (m, n) = F (m 1, n) + F (m, n 1) + F (m 1, n 1) k = k 1 + k 1 l l 1 l m + n = m + n 1 + m + n 1 m m 1 m C(m, n) = C(m 1, n) + C(m, n 1) F (m, n) C(m, n) = m + n m, 2n n 22n πn. Pairwise Alignment p.14/55
15 Dynamic Programming Approach F (i, j): the score for the best alignment between x 1... x i and y 1... y j. F (i, j) = max F (i 1, j 1) + 1, F (i 1, j 1) 1, F (i 1, j) 2, F (i, j 1) 2, x i = y i (match) x i y i (substitution) align x i with a gap align y j with a gap Pairwise Alignment p.15/55
16 { x1 x 2... x i 1 x i y 1 y 2... y j 1 y j F (i 1, j 1) + s(x i, y i ) { x1 x 2... x i 1 x i y 1 y 2... y j F (i 1, j) d { x1 x 2... x i y 1 y 2... y j 1 y j F (i, j 1) d Pairwise Alignment p.16/55
17 Alignment Graph F (i 1, j 1) F (i 1, j) +s(x i, y j ) d F (i, j 1) d F (i, j) Initial value: F (0, 0) = 0, F (0, j) = jd, F (i, 0) = id. Pairwise Alignment p.17/55
18 Example - a c c t g a a g c t a Pairwise Alignment p.18/55
19 Example - a c c t g a a g c t a backtrace Pairwise Alignment p.19/55
20 a c c t g a a g c t - a Pairwise Alignment p.20/55
21 Complexity 1. time = O(mn) 2. space= O(mn) if we need to find out the optimal alignment The problem for space is more serious when m and n are very large. Pairwise Alignment p.21/55
22 Linear-space Alignment Algorithm B(i, j): the best alignment score of the suffixes x m i+1... x m and y n j+1... y n F (i, j): forward matrix, B(i, j): backward matrix Then F (m, n) = max 0 k n {F (m 2, k) + B(m 2, n k)}. m 2 m 2 k n k Pairwise Alignment p.22/55
23 Algorithm 1. Compute F while saving the m 2 2. Compute B while saving the m 2 -th row. -th row. 3. Find the column k such that F ( m 2, k ) + B( m 2, n k ) = F (m, n). 4. Recursively partition the problem to two sub-problems: (a) Find the path from (0, 0) to ( m, 2 k ). (b) Find the path from ( m, 2 k ) to (m, n). Pairwise Alignment p.23/55
24 Example - a c c t g a a g c t a (F (i, j) matrix) Pairwise Alignment p.24/55
25 - a g t c c a a t c g a (B(i, j) matrix) Pairwise Alignment p.25/55
26 F ( m 2, k ) + B( m 2, n k ) = F (m, n). In this case, F (m, n) = 1 and k = 2. Hence, the best alignment of (acctga,agcta) is the concatenation of (ac,ag) and (ctga,cta). Pairwise Alignment p.26/55
27 Analysis of Complexity Clearly, the required space is O(min(m, n)). For time complexity, let T (m, n) be the time bound of the algorithm. Hence, we have T (m, n) = T ( m 2, k) + T ( m 2, n k) + O(mn) for some k. Pairwise Alignment p.27/55
28 T (m, n) = T ( m 2, k) + T (m 2, n k) + cmn) for some k. Suppose T (m, n) = αmn, then the right hand side becomes α m 2 k + αm αmn (n k) + cmn = + cmn. 2 2 Let α = 2c, then it equals to the left-hand side. Pairwise Alignment p.28/55
29 For more information on linear-space algorithms in pairwise alignment, see Chao, K. M., Hardison, R. C., and Miller, W Recent developments in linear-space alignment methods: a survey. Journal of Computational Biology, 1: Pairwise Alignment p.29/55
30 Revisiting Dynamic Programming Principle of optimality Recurrence Bottom up Pairwise Alignment p.30/55
31 Substitution matrices Suppose we have two models: 1. random model 2. match model Given any two aligned sequences x = x 1 x 2... x n y = y 1 y 2... y n where x i is aligned with y i. Pairwise Alignment p.31/55
32 In random model R, we suppose each letter a occurs independently with some frequency q a. Hence, Pr(x, y R) = q xi q yj. i j In match model M, letters a and b are aligned with joint probability p ab. Suppose residues a and b have been derived indep. from some unknown residue c. Hence, Pr(x, y M) = i p xi y i. Pairwise Alignment p.32/55
33 Define the odds ratio as Pr(x, y M) Pr(x, y R) = i q x i The log-odds ratio: i p x i y i j q y j = i p xi y i q xi q yi. S = i s(x i, y i ) where s(a, b) = log( p ab q a q b ). S > 0 means that x, y are more likely to be an instance of the match model. (Maximum Likelihood) BLOSUM & PAM matrices for proteins Pairwise Alignment p.33/55
34 PAM matrices 1. Dayhoff, Schwartz, Orcutt (1978) 2. The most widely used matrix is PAM250. Pairwise Alignment p.34/55
35 Pairwise Alignment p.35/55
36 BLOSUM Matrices 1. Henikoff & Henikoff (1992) 2. Derived from a set of aligned, ungapped regions from protein families called the BLOCKS database. 3. BLOSUM62 is the standard for ungapped matching. 4. BLOSUM50 is better for alignment with gaps. Pairwise Alignment p.36/55
37 BLOSUM50 Pairwise Alignment p.37/55
38 Pairwise Alignment Problems 1. Global alignment (Needleman & Wunsch, 1970) 2. Local alignment (Smith-Waterman, 1981) 3. End-space free alignment 4. Gap penality The version we currently used was due to Gotoh (1982). Pairwise Alignment p.38/55
39 Global Alignment Given two sequences x and y, what is the maximum similarity between them? Find a best alignment. Pairwise Alignment p.39/55
40 Local Alignment Given two sequences x and y, what is the maximum similarity between a subsequence of x and a subsequence of y? Find most similar subsequences. Pairwise Alignment p.40/55
41 End-space Free Alignment or Pairwise Alignment p.41/55
42 Global Alignment F (i, j) = max F (i 1, j 1) + s(x i, y j ), F (i 1, j) d, F (i, j 1) d. with initial value F (0, 0) = 0, F (0, j) = jd, F (i, 0) = id. And F (m, n) is the score. Pairwise Alignment p.42/55
43 Example Pairwise Alignment p.43/55
44 Local Alignment Motivation: Ignore stretches of non-coding DNA. Protein domains Pairwise Alignment p.44/55
45 Local Alignment F (i, j) = max 0, F (i 1, j 1) + s(x i, y j ), F (i 1, j) d, F (i, j 1) d. with initial value F (0, 0) = F (0, j) = F (i, 0) = 0. And the highest value of F (i, j) over the whole matrix is the score. Pairwise Alignment p.45/55
46 Example Pairwise Alignment p.46/55
47 Ends-free Alignment Motivation: shotgun sequence assembly Pairwise Alignment p.47/55
48 Ends-free Alignment F (i, j) = max F (i 1, j 1) + s(x i, y j ), F (i 1, j) d, F (i, j 1) d. with initial value F (0, 0) = F (0, j) = F (i, 0) = 0. And the highest value of F (i, j) in the last column F (i, n) or the last row F (m, j ) is the score. Pairwise Alignment p.48/55
49 Example Pairwise Alignment p.49/55
50 Complexity All of the above algorithms can be implemented in time O(mn) and in space O(m + n). Pairwise Alignment p.50/55
51 Gap Penality A gap is any maximal consecutive run of spaces in an alignment. The length of a gap is the number of indel operations in it. a t t c - - g a - t g g a c c a - - c g t g a t t c c Pairwise Alignment p.51/55
52 Motivation: Insertion or deletion of an entire sequence often occurs as a single mutation event. Two protein sequences might be relatively similar over several intervals. cdna: the complement of mrna Pairwise Alignment p.52/55
53 Gap Penality Models 1. constant gap penalty model: W g #gaps 2. affine gap penalty model: (y = ax + b) W g #gaps + W s #spaces 3. convex gap penalty model: W g + log(q) where q is the length of the gap. 4. arbitrary gap penalty model W g : gap-open penalty, W s : gap-extension penalty Pairwise Alignment p.53/55
54 Complexity 1. constant gap penalty model: Time= O(mn) 2. affine gap penalty model: Time= O(mn) 3. convex gap penalty model: Time= O(mn lg(m + n)) 4. arbitrary gap penalty model: Time = O(mn(m + n)) Pairwise Alignment p.54/55
55 Conclusion Pairwise Alignment p.55/55
Lecture 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 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 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 information20 Grundlagen der Bioinformatik, SS 08, D. Huson, May 27, Global and local alignment of two sequences using dynamic programming
20 Grundlagen der Bioinformatik, SS 08, D. Huson, May 27, 2008 4 Pairwise alignment We will discuss: 1. Strings 2. Dot matrix method for comparing sequences 3. Edit distance 4. Global and local alignment
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 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 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 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 information8 Grundlagen der Bioinformatik, SoSe 11, D. Huson, April 18, 2011
8 Grundlagen der Bioinformatik, SoSe 11, D. Huson, April 18, 2011 2 Pairwise alignment We will discuss: 1. Strings 2. Dot matrix method for comparing sequences 3. Edit distance and alignment 4. The number
More informationLocal Alignment: Smith-Waterman algorithm
Local Alignment: Smith-Waterman algorithm Example: a shared common domain of two protein sequences; extended sections of genomic DNA sequence. Sensitive to detect similarity in highly diverged sequences.
More information8 Grundlagen der Bioinformatik, SS 09, D. Huson, April 28, 2009
8 Grundlagen der Bioinformatik, SS 09, D. Huson, April 28, 2009 2 Pairwise alignment We will discuss: 1. Strings 2. Dot matrix method for comparing sequences 3. Edit distance and alignment 4. The number
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 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 informationPractical considerations of working with sequencing data
Practical considerations of working with sequencing data File Types Fastq ->aligner -> reference(genome) coordinates Coordinate files SAM/BAM most complete, contains all of the info in fastq and more!
More informationPairwise alignment, Gunnar Klau, November 9, 2005, 16:
Pairwise alignment, Gunnar Klau, November 9, 2005, 16:36 2012 2.1 Growth rates For biological sequence analysis, we prefer algorithms that have time and space requirements that are linear in the length
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 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 informationSingle alignment: Substitution Matrix. 16 march 2017
Single alignment: Substitution Matrix 16 march 2017 BLOSUM Matrix BLOSUM Matrix [2] (Blocks Amino Acid Substitution Matrices ) It is based on the amino acids substitutions observed in ~2000 conserved block
More informationAlgorithms in Bioinformatics: A Practical Introduction. Sequence Similarity
Algorithms in Bioinformatics: A Practical Introduction Sequence Similarity Earliest Researches in Sequence Comparison Doolittle et al. (Science, July 1983) searched for platelet-derived growth factor (PDGF)
More informationAnalysis and Design of Algorithms Dynamic Programming
Analysis and Design of Algorithms Dynamic Programming Lecture Notes by Dr. Wang, Rui Fall 2008 Department of Computer Science Ocean University of China November 6, 2009 Introduction 2 Introduction..................................................................
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 informationSequence Comparison. mouse human
Sequence Comparison Sequence Comparison mouse human Why Compare Sequences? The first fact of biological sequence analysis In biomolecular sequences (DNA, RNA, or amino acid sequences), high sequence similarity
More informationBio nformatics. Lecture 3. Saad Mneimneh
Bio nformatics Lecture 3 Sequencing As before, DNA is cut into small ( 0.4KB) fragments and a clone library is formed. Biological experiments allow to read a certain number of these short fragments per
More informationCollected Works of Charles Dickens
Collected Works of Charles Dickens A Random Dickens Quote If there were no bad people, there would be no good lawyers. Original Sentence It was a dark and stormy night; the night was dark except at sunny
More informationBioinformatics. Scoring Matrices. David Gilbert Bioinformatics Research Centre
Bioinformatics Scoring Matrices David Gilbert Bioinformatics Research Centre www.brc.dcs.gla.ac.uk Department of Computing Science, University of Glasgow Learning Objectives To explain the requirement
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 informationMotivating the need for optimal sequence alignments...
1 Motivating the need for optimal sequence alignments... 2 3 Note that this actually combines two objectives of optimal sequence alignments: (i) use the score of the alignment o infer homology; (ii) use
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 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 informationLecture 5: September Time Complexity Analysis of Local Alignment
CSCI1810: Computational Molecular Biology Fall 2017 Lecture 5: September 21 Lecturer: Sorin Istrail Scribe: Cyrus Cousins Note: LaTeX template courtesy of UC Berkeley EECS dept. Disclaimer: These notes
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 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 informationPairwise Sequence Alignment
Introduction to Bioinformatics Pairwise Sequence Alignment Prof. Dr. Nizamettin AYDIN naydin@yildiz.edu.tr Outline Introduction to sequence alignment pair wise sequence alignment The Dot Matrix Scoring
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 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 informationFirst generation sequencing and pairwise alignment (High-tech, not high throughput) Analysis of Biological Sequences
First generation sequencing and pairwise alignment (High-tech, not high throughput) Analysis of Biological Sequences 140.638 where do sequences come from? DNA is not hard to extract (getting DNA from a
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 informationEvolution. CT Amemiya et al. Nature 496, (2013) doi: /nature12027
Sequence Alignment Evolution CT Amemiya et al. Nature 496, 311-316 (2013) doi:10.1038/nature12027 Evolutionary Rates next generation OK OK OK X X Still OK? Sequence conservation implies function 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 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 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 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 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 informationAn Introduction to Sequence Similarity ( Homology ) Searching
An Introduction to Sequence Similarity ( Homology ) Searching Gary D. Stormo 1 UNIT 3.1 1 Washington University, School of Medicine, St. Louis, Missouri ABSTRACT Homologous sequences usually have the same,
More informationLecture 2, 5/12/2001: Local alignment the Smith-Waterman algorithm. Alignment scoring schemes and theory: substitution matrices and gap models
Lecture 2, 5/12/2001: Local alignment the Smith-Waterman algorithm Alignment scoring schemes and theory: substitution matrices and gap models 1 Local sequence alignments Local sequence alignments are necessary
More informationC E N T R. Introduction to bioinformatics 2007 E B I O I N F O R M A T I C S V U F O R I N T. Lecture 5 G R A T I V. Pair-wise Sequence Alignment
C E N T R E F O R I N T E G R A T I V E B I O I N F O R M A T I C S V U Introduction to bioinformatics 2007 Lecture 5 Pair-wise Sequence Alignment Bioinformatics Nothing in Biology makes sense except in
More informationScoring Matrices. Shifra Ben-Dor Irit Orr
Scoring Matrices Shifra Ben-Dor Irit Orr Scoring matrices Sequence alignment and database searching programs compare sequences to each other as a series of characters. All algorithms (programs) for comparison
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 informationPairwise alignment using HMMs
Pairwise alignment using HMMs The states of an HMM fulfill the Markov property: probability of transition depends only on the last state. CpG islands and casino example: HMMs emit sequence of symbols (nucleotides
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 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 informationSimilarity or Identity? When are molecules similar?
Similarity or Identity? When are molecules similar? Mapping Identity A -> A T -> T G -> G C -> C or Leu -> Leu Pro -> Pro Arg -> Arg Phe -> Phe etc If we map similarity using identity, how similar are
More informationBioinformatics and BLAST
Bioinformatics and BLAST Overview Recap of last time Similarity discussion Algorithms: Needleman-Wunsch Smith-Waterman BLAST Implementation issues and current research Recap from Last Time Genome consists
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 informationPairwise alignment. 2.1 Introduction GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD----LHAHKL
2 Pairwise alignment 2.1 Introduction The most basic sequence analysis task is to ask if two sequences are related. This is usually done by first aligning the sequences (or parts of them) and then deciding
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 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 informationAlignment principles and homology searching using (PSI-)BLAST. Jaap Heringa Centre for Integrative Bioinformatics VU (IBIVU)
Alignment principles and homology searching using (PSI-)BLAST Jaap Heringa Centre for Integrative Bioinformatics VU (IBIVU) http://ibivu.cs.vu.nl Bioinformatics Nothing in Biology makes sense except in
More informationBiologically significant sequence alignments using Boltzmann probabilities
Biologically significant sequence alignments using Boltzmann probabilities P. Clote Department of Biology, Boston College Gasson Hall 416, Chestnut Hill MA 02467 clote@bc.edu May 7, 2003 Abstract In this
More informationEECS730: Introduction to Bioinformatics
EECS730: Introduction to Bioinformatics Lecture 05: Index-based alignment algorithms Slides adapted from Dr. Shaojie Zhang (University of Central Florida) Real applications of alignment Database search
More informationSequence Database Search Techniques I: Blast and PatternHunter tools
Sequence Database Search Techniques I: Blast and PatternHunter tools Zhang Louxin National University of Singapore Outline. Database search 2. BLAST (and filtration technique) 3. PatternHunter (empowered
More informationLecture 1, 31/10/2001: Introduction to sequence alignment. The Needleman-Wunsch algorithm for global sequence alignment: description and properties
Lecture 1, 31/10/2001: Introduction to sequence alignment The Needleman-Wunsch algorithm for global sequence alignment: description and properties 1 Computational sequence-analysis The major goal of computational
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 informationComputational Molecular Biology
Computational Molecular Biology Shivam Nadimpalli Last updated: December 6, 2018 Hello! These are notes for CS 181 Computational Molecular Biology at Brown University, taught by Professor Sorin Istrail
More informationAlignment & BLAST. By: Hadi Mozafari KUMS
Alignment & BLAST By: Hadi Mozafari KUMS SIMILARITY - ALIGNMENT Comparison of primary DNA or protein sequences to other primary or secondary sequences Expecting that the function of the similar sequence
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 informationBINF 730. DNA Sequence Alignment Why?
BINF 730 Lecture 2 Seuence Alignment DNA Seuence Alignment Why? Recognition sites might be common restriction enzyme start seuence stop seuence other regulatory seuences Homology evolutionary common progenitor
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 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 informationLecture 4: September 19
CSCI1810: Computational Molecular Biology Fall 2017 Lecture 4: September 19 Lecturer: Sorin Istrail Scribe: Cyrus Cousins Note: LaTeX template courtesy of UC Berkeley EECS dept. Disclaimer: These notes
More informationIntroduction to Computation & Pairwise Alignment
Introduction to Computation & Pairwise Alignment Eunok Paek eunokpaek@hanyang.ac.kr Algorithm what you already know about programming Pan-Fried Fish with Spicy Dipping Sauce This spicy fish dish is quick
More informationIntroduction to sequence alignment. Local alignment the Smith-Waterman algorithm
Lecture 2, 12/3/2003: Introduction to sequence alignment The Needleman-Wunsch algorithm for global sequence alignment: description and properties Local alignment the Smith-Waterman algorithm 1 Computational
More informationAlgorithm Design and Analysis
Algorithm Design and Analysis LECTURE 18 Dynamic Programming (Segmented LS recap) Longest Common Subsequence Adam Smith Segmented Least Squares Least squares. Foundational problem in statistic and numerical
More informationString Matching Problem
String Matching Problem Pattern P Text T Set of Locations L 9/2/23 CAP/CGS 5991: Lecture 2 Computer Science Fundamentals Specify an input-output description of the problem. Design a conceptual algorithm
More information... and searches for related sequences probably make up the vast bulk of bioinformatics activities.
1 2 ... and searches for related sequences probably make up the vast bulk of bioinformatics activities. 3 The terms homology and similarity are often confused and used incorrectly. Homology is a quality.
More informationSequence Alignment Techniques and Their Uses
Sequence Alignment Techniques and Their Uses Sarah Fiorentino Since rapid sequencing technology and whole genomes sequencing, the amount of sequence information has grown exponentially. With all of this
More informationAlignment Algorithms. Alignment Algorithms
Midterm Results Big improvement over scores from the previous two years. Since this class grade is based on the previous years curve, that means this class will get higher grades than the previous years.
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 informationLarge-Scale Genomic Surveys
Bioinformatics Subtopics Fold Recognition Secondary Structure Prediction Docking & Drug Design Protein Geometry Protein Flexibility Homology Modeling Sequence Alignment Structure Classification Gene Prediction
More informationMinimum Edit Distance. Defini'on of Minimum Edit Distance
Minimum Edit Distance Defini'on of Minimum Edit Distance How similar are two strings? Spell correc'on The user typed graffe Which is closest? graf gra@ grail giraffe Computa'onal Biology Align two sequences
More information2 Pairwise alignment. 2.1 References. 2.2 Importance of sequence alignment. Introduction to the pairwise sequence alignment problem.
2 Pairwise alignment Introduction to the pairwise sequence alignment problem Dot plots Scoring schemes The principle of dynamic programming Alignment algorithms based on dynamic programming 2.1 References
More informationFinding the Best Biological Pairwise Alignment Through Genetic Algorithm Determinando o Melhor Alinhamento Biológico Através do Algoritmo Genético
Finding the Best Biological Pairwise Alignment Through Genetic Algorithm Determinando o Melhor Alinhamento Biológico Através do Algoritmo Genético Paulo Mologni 1, Ailton Akira Shinoda 2, Carlos Dias Maciel
More informationModule: Sequence Alignment Theory and Applications Session: Introduction to Searching and Sequence Alignment
Module: Sequence Alignment Theory and Applications Session: Introduction to Searching and Sequence Alignment Introduction to Bioinformatics online course : IBT Jonathan Kayondo Learning Objectives Understand
More informationLinear-Space Alignment
Linear-Space Alignment Subsequences and Substrings Definition A string x is a substring of a string x, if x = ux v for some prefix string u and suffix string v (similarly, x = x i x j, for some 1 i j x
More informationCSE 202 Dynamic Programming II
CSE 202 Dynamic Programming II Chapter 6 Dynamic Programming Slides by Kevin Wayne. Copyright 2005 Pearson-Addison Wesley. All rights reserved. 1 Algorithmic Paradigms Greed. Build up a solution incrementally,
More informationIntroduction to Bioinformatics
Introduction to Bioinformatics Jianlin Cheng, PhD Department of Computer Science Informatics Institute 2011 Topics Introduction Biological Sequence Alignment and Database Search Analysis of gene expression
More informationHomology Modeling (Comparative Structure Modeling) GBCB 5874: Problem Solving in GBCB
Homology Modeling (Comparative Structure Modeling) Aims of Structural Genomics High-throughput 3D structure determination and analysis To determine or predict the 3D structures of all the proteins encoded
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 informationChapter 5. Proteomics and the analysis of protein sequence Ⅱ
Proteomics Chapter 5. Proteomics and the analysis of protein sequence Ⅱ 1 Pairwise similarity searching (1) Figure 5.5: manual alignment One of the amino acids in the top sequence has no equivalent and
More informationApproximation: Theory and Algorithms
Approximation: Theory and Algorithms The String Edit Distance Nikolaus Augsten Free University of Bozen-Bolzano Faculty of Computer Science DIS Unit 2 March 6, 2009 Nikolaus Augsten (DIS) Approximation:
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 informationAlgorithms in Bioinformatics I, ZBIT, Uni Tübingen, Daniel Huson, WS 2003/4 1
Algorithms in Bioinformatics I, ZBIT, Uni Tübingen, Daniel Huson, WS 2003/4 1 Algorithms in Bioinformatics I Winter Semester 2003/4, Center for Bioinformatics Tübingen, WSI-Informatik, Universität Tübingen
More informationWeek 10: Homology Modelling (II) - HHpred
Week 10: Homology Modelling (II) - HHpred Course: Tools for Structural Biology Fabian Glaser BKU - Technion 1 2 Identify and align related structures by sequence methods is not an easy task All comparative
More informationCS 580: Algorithm Design and Analysis
CS 58: Algorithm Design and Analysis Jeremiah Blocki Purdue University Spring 28 Announcement: Homework 3 due February 5 th at :59PM Midterm Exam: Wed, Feb 2 (8PM-PM) @ MTHW 2 Recap: Dynamic Programming
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 informationPairwise sequence alignment and pair hidden Markov models
Pairwise sequence alignment and pair hidden Markov models Martin C. Frith April 13, 2012 ntroduction Pairwise alignment and pair hidden Markov models (phmms) are basic textbook fare [2]. However, there
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 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 informationStudy and Implementation of Various Techniques Involved in DNA and Protein Sequence Analysis
Study and Implementation of Various Techniques Involved in DNA and Protein Sequence Analysis Kumud Joseph Kujur, Sumit Pal Singh, O.P. Vyas, Ruchir Bhatia, Varun Singh* Indian Institute of Information
More information