An Improved Search Algorithm for Optimal Multiple-Sequence Alignment Paper by: Stefan Schroedl Presentation by: Bryan Franklin.

Slides:

Advertisements

Similar presentations

Pairwise Sequence Alignment Sushmita Roy BMI/CS 576 Sushmita Roy Sep 10 th, 2013 BMI/CS 576.

Advertisements

Parallel BioInformatics Sathish Vadhiyar. Parallel Bioinformatics  Many large scale applications in bioinformatics – sequence search, alignment, construction.

DYNAMIC PROGRAMMING ALGORITHMS VINAY ABHISHEK MANCHIRAJU.

1 Introduction to Sequence Analysis Utah State University – Spring 2012 STAT 5570: Statistical Bioinformatics Notes 6.1.

1 ALIGNMENT OF NUCLEOTIDE & AMINO-ACID SEQUENCES.

Sequence Similarity Searching Class 4 March 2010.

Expect value Expect value (E-value) Expected number of hits, of equivalent or better score, found by random chance in a database of the size.

Sequence Alignment.

Geometric Crossover for Biological Sequences Alberto Moraglio, Riccardo Poli & Rolv Seehuus EuroGP 2006.

Introduction to Bioinformatics Algorithms Sequence Alignment.

Population New Population Selection Crossover and Mutation Insert When the new population is full repeat Generational Algorithm.

Reminder -Structure of a genome Human 3x10 9 bp Genome: ~30,000 genes ~200,000 exons ~23 Mb coding ~15 Mb noncoding pre-mRNA transcription splicing translation.

Sequence similarity.

Sequence Alignment III CIS 667 February 10, 2004.

Implementation of Planted Motif Search Algorithms PMS1 and PMS2 Clifford Locke BioGrid REU, Summer 2008 Department of Computer Science and Engineering.

Aligning Alignments Exactly By John Kececioglu, Dean Starrett CS Dept. Univ. of Arizona Appeared in 8 th ACM RECOME 2004, Presented by Jie Meng.

. Computational Genomics Lecture #3a (revised 24/3/09) This class has been edited from Nir Friedman’s lecture which is available at

Introduction to Bioinformatics Algorithms Sequence Alignment.

Bioinformatics Unit 1: Data Bases and Alignments Lecture 3: “Homology” Searches and Sequence Alignments (cont.) The Mechanics of Alignments.

Dynamic Programming. Pairwise Alignment Needleman - Wunsch Global Alignment Smith - Waterman Local Alignment.

Incorporating Bioinformatics in an Algorithms Course Lawrence D’Antonio Ramapo College of New Jersey.

15-853:Algorithms in the Real World

Alignment methods II April 24, 2007 Learning objectives- 1) Understand how Global alignment program works using the longest common subsequence method.

TM Biological Sequence Comparison / Database Homology Searching Aoife McLysaght Summer Intern, Compaq Computer Corporation Ballybrit Business Park, Galway,

Alignment Statistics and Substitution Matrices BMI/CS 576 Colin Dewey Fall 2010.

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

Sequence Alignment.

Sequence Analysis Alignments dot-plots scoring scheme Substitution matrices Search algorithms (BLAST)

BIOMETRICS Module Code: CA641 Week 11- Pairwise Sequence Alignment.

Brandon Andrews.  Longest Common Subsequences  Global Sequence Alignment  Scoring Alignments  Local Sequence Alignment  Alignment with Gap Penalties.

. Sequence Alignment and Database Searching 2 Biological Motivation u Inference of Homology  Two genes are homologous if they share a common evolutionary.

The dynamic nature of the proteome

Some Independent Study on Sequence Alignment — Lan Lin prepared for theory group meeting on July 16, 2003.

1 Generalized Tree Alignment: The Deferred Path Heuristic Stinus Lindgreen

BLAST: A Case Study Lecture 25. BLAST: Introduction The Basic Local Alignment Search Tool, BLAST, is a fast approach to finding similar strings of characters.

Introduction to Bioinformatics Algorithms Sequence Alignment.

Sequence Alignment Goal: line up two or more sequences An alignment of two amino acid sequences: …. Seq1: HKIYHLQSKVPTFVRMLAPEGALNIHEKAWNAYPYCRTVITN-EYMKEDFLIKIETWHKP.

Pairwise Sequence Alignment (II) (Lecture for CS498-CXZ Algorithms in Bioinformatics) Sept. 27, 2005 ChengXiang Zhai Department of Computer Science University.

. Sequence Alignment. Sequences Much of bioinformatics involves sequences u DNA sequences u RNA sequences u Protein sequences We can think of these sequences.

Pairwise alignment of DNA/protein sequences I519 Introduction to Bioinformatics, Fall 2012.

Sequence Analysis CSC 487/687 Introduction to computing for Bioinformatics.

Alignment, Part I Vasileios Hatzivassiloglou University of Texas at Dallas.

Computational Molecular Biology Introduction and Preliminaries.

Construction of Substitution Matrices

Multiple Sequence Alignment. How to score a MSA? Very commonly: Sum of Pairs = SP Compute the pairwise score of all pairs of sequences and sum them. Gap.

Chapter 3 Computational Molecular Biology Michael Smith

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

Approximation Algorithms For Protein Folding Prediction Giancarlo MAURI,Antonio PICCOLBONI and Giulio PAVESI Symposium on Discrete Algorithms, pp ,

1 Sequence Alignment Input: two sequences over the same alphabet Output: an alignment of the two sequences Example: u GCGCATGGATTGAGCGA u TGCGCCATTGATGACCA.

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 Sequence Alignment Xingquan Zhu Dept. of Computer Science and Engineering.

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

Biocomputation: Comparative Genomics Tanya Talkar Lolly Kruse Colleen O’Rourke.

Sequence Alignment.

Construction of Substitution matrices

GA for Sequence Alignment  Pair-wise alignment  Multiple string alignment.

Lecture 1 BNFO 601 Usman Roshan. Course overview Perl progamming language (and some Unix basics) –Unix basics –Intro Perl exercises –Dynamic programming.

. Sequence Alignment Author:- Aya Osama Supervision:- Dr.Noha khalifa.

DNA sequences alignment measurement Lecture 13. Introduction Measurement of “strength” alignment Nucleic acid and amino acid substitutions Measurement.

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

Substitution Matrices and Alignment Statistics BMI/CS 776 Mark Craven February 2002.

Bioinformatics Overview

Wednesday March 22, 2017 I can: Agenda Catalyst HW: IP: Mutations

Multiple sequence alignment (msa)

Types of Mutations.

LSM3241: Bioinformatics and Biocomputing Lecture 4: Sequence analysis methods revisited Prof. Chen Yu Zong Tel:

Sequence Alignment Using Dynamic Programming

Intro to Alignment Algorithms: Global and Local

Sequence Analysis Alan Christoffels

Presentation transcript:

An Improved Search Algorithm for Optimal Multiple-Sequence Alignment Paper by: Stefan Schroedl Presentation by: Bryan Franklin

Outline Multiple-Sequence Alignment (MSA) Graph Representation Computing Path Costs Heuristics Experimental Results Other Optimizations

Multiple-Sequence-Alignment Sequence: DNA: String over alphabet {A,C,G,T} Protein: String with |Σ|=20 (one symbol for each amino acid) Alignment: Insert gaps (_) into sequences to line up matching characters.

Multiple-Sequence-Alignment Sequences: ABCB, BCD, DB

Multiple-Sequence-Alignment Indel: Insertion, Deletion, Point mutation (single symbol replacement) Find a minimum set of indels between two or more sequences. NP-Hard for an arbitrary number of sequences

Multiple-Sequence-Alignment Applications Common ancestry between species Locating useful portions of DNA Predicting structure of folded proteins

Graph Representation

Computing G(n) Considerations Biological Meaning Cost of computation Sum-of-pairs Substitution matrix ((|Σ|+1) 2 ) Sum alignment costs for all pairs Costs can depend on neighbors

Computing G(n) Sequences: ABCB, BCD, DB

Computing G(n)

Heuristics Methods Examined 2-fold (h pair ) divide-conquer 3-fold (h 3,all ) 4-fold (h 4,all )

Heuristic Comparison

Resource Usage

Optimizations Sparse Path Representation Curve fitting for predicting threshold values Sub-optimal paths periodically deleted

The End Any Questions?