Multiple sequence alignment (msa)

Slides:

Advertisements

Similar presentations

Multiple Sequence Alignment Dynamic Programming. Multiple Sequence Alignment VTISCTGSSSNIGAG  NHVKWYQQLPG VTISCTGTSSNIGS  ITVNWYQQLPG LRLSCSSSGFIFSS.

Advertisements

Multiple Alignment Anders Gorm Pedersen Molecular Evolution Group

Bioinformatics Multiple sequence alignments Scoring multiple sequence alignments Progressive methods ClustalW Other methods Hidden Markov Models Lecture.

Hidden Markov Model in Biological Sequence Analysis – Part 2

Blast to Psi-Blast Blast makes use of Scoring Matrix derived from large number of proteins. What if you want to find homologs based upon a specific gene.

BNFO 602 Multiple sequence alignment Usman Roshan.

Introduction to Bioinformatics Burkhard Morgenstern Institute of Microbiology and Genetics Department of Bioinformatics Goldschmidtstr. 1 Göttingen, March.

1 “INTRODUCTION TO BIOINFORMATICS” “SPRING 2005” “Dr. N AYDIN” Lecture 4 Multiple Sequence Alignment Doç. Dr. Nizamettin AYDIN

. Class 5: Multiple Sequence Alignment. Multiple sequence alignment VTISCTGSSSNIGAG-NHVKWYQQLPG VTISCTGTSSNIGS--ITVNWYQQLPG LRLSCSSSGFIFSS--YAMYWVRQAPG.

Sequence analysis lecture 6 Sequence analysis course Lecture 6 Multiple sequence alignment 2 of 3 Multiple alignment methods.

Multiple Sequence Alignment Algorithms in Computational Biology Spring 2006 Most of the slides were created by Dan Geiger and Ydo Wexler and edited by.

Multiple alignment June 29, 2007 Learning objectives- Review sequence alignment answer and answer questions you may have. Understand how the E value may.

What you should know by now Concepts: Pairwise alignment Global, semi-global and local alignment Dynamic programming Sequence similarity (Sum-of-Pairs)

Lecture 9 Hidden Markov Models BioE 480 Sept 21, 2004.

BNFO 240 Usman Roshan. Last time Traceback for alignment How to select the gap penalties? Benchmark alignments –Structural superimposition –BAliBASE.

Performance Optimization of Clustal W: Parallel Clustal W, HT Clustal and MULTICLUSTAL Arunesh Mishra CMSC 838 Presentation Authors : Dmitri Mikhailov,

Multiple alignment: heuristics

Multiple sequence alignment

Similar Sequence Similar Function Charles Yan Spring 2006.

Sequence Alignment III CIS 667 February 10, 2004.

BNFO 602 Multiple sequence alignment Usman Roshan.

PAM250. M. Dayhoff Scoring Matrices Point Accepted Mutations or PAM matrices Proteins with 85% identity were used -> the function is not significantly.

Alignment III PAM Matrices. 2 PAM250 scoring matrix.

Multiple Sequence Alignments

Multiple sequence alignment methods 1 Corné Hoogendoorn Denis Miretskiy.

CECS Introduction to Bioinformatics University of Louisville Spring 2003 Dr. Eric Rouchka Lecture 3: Multiple Sequence Alignment Eric C. Rouchka,

CISC667, F05, Lec8, Liao CISC 667 Intro to Bioinformatics (Fall 2005) Multiple Sequence Alignment Scoring Dynamic Programming algorithms Heuristic algorithms.

Introduction to Bioinformatics From Pairwise to Multiple Alignment.

Chapter 5 Multiple Sequence Alignment.

Multiple Sequence Alignment BMI/CS 576 Colin Dewey Fall 2010.

Multiple Sequence Alignment CSC391/691 Bioinformatics Spring 2004 Fetrow/Burg/Miller (Slides by J. Burg)

Multiple sequence alignment

Multiple Sequence Alignment

Pair-wise Sequence Alignment What happened to the sequences of similar genes? random mutation deletion, insertion Seq. 1: 515 EVIRMQDNNPFSFQSDVYSYG EVI.

CISC667, S07, Lec5, Liao CISC 667 Intro to Bioinformatics (Spring 2007) Pairwise sequence alignment Needleman-Wunsch (global alignment)

Multiple Alignment and Phylogenetic Trees Csc 487/687 Computing for Bioinformatics.

Eric C. Rouchka, University of Louisville SATCHMO: sequence alignment and tree construction using hidden Markov models Edgar, R.C. and Sjolander, K. Bioinformatics.

Pairwise Sequence Alignment. The most important class of bioinformatics tools – pairwise alignment of DNA and protein seqs. alignment 1alignment 2 Seq.

Eidhammer et al. Protein Bioinformatics Chapter 4 1 Multiple Global Sequence Alignment and Phylogenetic trees Inge Jonassen and Ingvar Eidhammer.

Multiple Sequence Alignments Craig A. Struble, Ph.D. Department of Mathematics, Statistics, and Computer Science Marquette University.

Construction of Substitution Matrices

Bioinformatics Multiple Alignment. Overview Introduction Multiple Alignments Global multiple alignment –Introduction –Scoring –Algorithms.

Multiple alignment: Feng- Doolittle algorithm. Why multiple alignments? Alignment of more than two sequences Usually gives better information about conserved.

Multiple Alignment and Phylogenetic Trees Csc 487/687 Computing for Bioinformatics.

Intro to Alignment Algorithms: Global and Local Intro to Alignment Algorithms: Global and Local Algorithmic Functions of Computational Biology Professor.

COT 6930 HPC and Bioinformatics Multiple Sequence Alignment Xingquan Zhu Dept. of Computer Science and Engineering.

Doug Raiford Lesson 5.  Dynamic programming methods  Needleman-Wunsch (global alignment)  Smith-Waterman (local alignment)  BLAST Fixed: best Linear:

Pairwise sequence alignment Lecture 02. Overview  Sequence comparison lies at the heart of bioinformatics analysis.  It is the first step towards structural.

Sequence Alignment.

Burkhard Morgenstern Institut für Mikrobiologie und Genetik Molekulare Evolution und Rekonstruktion von phylogenetischen Bäumen WS 2006/2007.

Construction of Substitution matrices

1 Multiple Sequence Alignment(MSA). 2 Multiple Alignment Number of sequences >2 Global alignment Seek an alignment that maximizes score.

V diagonal lines give equivalent residues ILS TRIVHVNSILPSTN V I L S T R I V I L P E F S T Sequence A Sequence B Dot Plots, Path Matrices, Score Matrices.

V diagonal lines give equivalent residues ILS TRIVHVNSILPSTN V I L S T R I V I L P E F S T Sequence A Sequence B Dot Plots, Path Matrices, Score Matrices.

Multiple Sequence Alignment (cont.) (Lecture for CS397-CXZ Algorithms in Bioinformatics) Feb. 13, 2004 ChengXiang Zhai Department of Computer Science University.

More on HMMs and Multiple Sequence Alignment BMI/CS 776 Mark Craven March 2002.

Techniques for Protein Sequence Alignment and Database Searching G P S Raghava Scientist & Head Bioinformatics Centre, Institute of Microbial Technology,

Multiple Sequence Alignment Dr. Urmila Kulkarni-Kale Bioinformatics Centre University of Pune

Pairwise alignment Now we know how to do it: How do we get a multiple alignment (three or more sequences)? Multiple alignment: much greater combinatorial.

Bioinformatics Overview

The ideal approach is simultaneous alignment and tree estimation.

Multiple Sequence Alignment

Sequence Alignment 11/24/2018.

Intro to Alignment Algorithms: Global and Local

In Bioinformatics use a computational method - Dynamic Programming.

Multiple Sequence Alignment (I)

Introduction to Bioinformatics

Computational Genomics Lecture #3a

MULTIPLE SEQUENCE ALIGNMENT

Presentation transcript:

Multiple sequence alignment (msa) Lecture 8 CS566

Motivation “Two swallows do not make a summer” Discover conserved regions Predict important regions of the protein Discover domains Search for additional members of a protein family (profile-based searching) Build phylogenetic trees Lecture 8 CS566

Topics Scoring schemes Optimal Heuristic algorithms Pairwise N-way Multidimensional dynamic programming Heuristic algorithms Progressive Iterative Lecture 8 CS566

Scoring schemes Alignment score = l Cl Column Score Cl Ideally Based on n-way joint probability (n-generalized AAS) Sum of Pairs i<j sij Based on amino acid substitution matrices Gap-gap = 0; Gap-char = -g Commonest scheme used Fallacious: Assumes only 2-way and not n-way joint probabilities Score not proportional to number of sequences in alignment N-way sums Need to know central point of reference (ancestral sequence) Lecture 8 CS566

Multidimensional Dynamic Programming Line up n sequences in a grid having n dimensions Score each cell as the maximum of Lining up all corresponding characters AND All possible combinations of gaps and characters Note choice made Reconstruct alignment by traceback Global or Local dynamic programming? Space complexity? Time complexity? Lecture 8 CS566

MSA – Efficient Multidimensional Dynamic Programming Carillo-Lipman MSA algorithm Uses pair-wise dynamic programming to identify sub-matrix regions of near-optimality n-dimensional dynamic programming carried out within space of intersection of near-optimal regions Still limited to only a few sequences Is this an optimal algorithm or not? Lecture 8 CS566

Progressive alignment New concepts Consider aligning alignments to alignments/sequences en bloc Hierarchical/Sequential order of alignment (“Once a cobbler, always a cobbler”) Heuristic Fast Lecture 8 CS566

Progressive alignment - Clustal Compute all pairwise alignments Convert alignment scores into distances Build guide tree (phylogenetic tree) Align sequences in order suggested by ‘guide tree’ Position specific scoring system used Gap costs depend on position Composition based scoring system used Percentage similarity dictates choice of scoring matrix Weighting based on composition bias Only ‘cross-terms’ (profile-profile) used in scoring Lecture 8 CS566

Progressive alignment - Clustal ClustalV (Now history!) ClustalW (Takes weighting into account for composition bias) ClustalX (Graphical interface) Lecture 8 CS566

Iterative refinement-1 “Once a cobbler, now a king!” Iterative algorithm: Compute all pairwise similarities Start with best pair Add ‘most-similar’ sequence to profile successively till none left Remove and re-align each sequence till convergence Lecture 8 CS566

Iterative refinement-2 Genetic programming-based msa Create initial random alignment Score alignment Retain better scoring half of alignment Mutate remaining half of alignment with ideas from genetic recombination Random gap insertion En bloc shifts Probabilistic order of alignment Score resulting alignment Iterate till convergence Lecture 8 CS566