Splicing Exons: A Eukaryotic Challenge to Gene Prediction Ian McCoy.

Slides:

Advertisements

Similar presentations

Gene Prediction: Similarity-Based Approaches

Advertisements

1. Find the cost of each of the following using the Nearest Neighbor Algorithm. a)Start at Vertex M.

Sorting by reversals Bogdan Pasaniuc Dept. of Computer Science & Engineering.

CHAPTER 7 Greedy Algorithms.

Minimum Clique Partition Problem with Constrained Weight for Interval Graphs Jianping Li Department of Mathematics Yunnan University Jointed by M.X. Chen.

Lower Bound for Sparse Euclidean Spanners Presented by- Deepak Kumar Gupta(Y6154), Nandan Kumar Dubey(Y6279), Vishal Agrawal(Y6541)

Max- coloring in trees SRIRAM V.PEMMARAJU AND RAJIV RAMAN BY JAYATI JENNIFER LAW.

CS 206 Introduction to Computer Science II 04 / 01 / 2009 Instructor: Michael Eckmann.

Approximations of points and polygonal chains

Genomics: READING genome sequences ASSEMBLY of the sequence ANNOTATION of the sequence carry out dideoxy sequencing connect seqs. to make whole chromosomes.

Comp 122, Spring 2004 Greedy Algorithms. greedy - 2 Lin / Devi Comp 122, Fall 2003 Overview  Like dynamic programming, used to solve optimization problems.

Minimum Spanning Tree Sarah Brubaker Tuesday 4/22/8.

Greedy Algorithms CS 6030 by Savitha Parur Venkitachalam.

Introduction to Bioinformatics Algorithms Divide & Conquer Algorithms.

Introduction to Bioinformatics Algorithms Divide & Conquer Algorithms.

Introduction to Bioinformatics Algorithms Divide & Conquer Algorithms.

Presented By Dr. Shazzad Hosain Asst. Prof. EECS, NSU Multiple Sequence Alignment Motif Finding and Gene Prediction.

Designing Algorithms Csci 107 Lecture 4. Outline Last time Computing 1+2+…+n Adding 2 n-digit numbers Today: More algorithms Sequential search Variations.

Gene Prediction: Similarity-Based Approaches (selected from Jones/Pevzner lecture notes)

The Motif Problem Paul Tamashiro School of Mathematics Georgia Institute of Technology April 16, 2008.

Improved Image Quilting Jeremy Long David Mould. Introduction   Goal: improve “ minimum error boundary cut ”

How many transcripts does it take to reconstruct the splice graph? Introduction Alternative splicing is the process by which a single gene may be used.

Protein Sequencing and Identification by Mass Spectrometry.

Dynamic Programming Reading Material: Chapter 7..

Introduction to Bioinformatics Algorithms Greedy Algorithms And Genome Rearrangements.

Sequence Alignment Bioinformatics. Sequence Comparison Problem: Given two sequences S & T, are S and T similar? Need to establish some notion of similarity.

1 Sorting by Transpositions Based on the First Increasing Substring Concept Advisor: Professor R.C.T. Lee Speaker: Ming-Chiang Chen.

Phylogenetic Tree Construction and Related Problems Bioinformatics.

1 Theory I Algorithm Design and Analysis (11 - Edit distance and approximate string matching) Prof. Dr. Th. Ottmann.

Sequence comparison: Local alignment

Dynamic Programming (cont’d) CS 466 Saurabh Sinha.

Dynamic Programming II

An Introduction to Bioinformatics Algorithmswww.bioalgorithms.info Gene Prediction: Similarity-Based Approaches.

Presented by Liu Qi An introduction to Bioinformatics Algorithms Qi Liu

Math – Getting Information from the Graph of a Function 1.

Sequence Alignment.

Space-Efficient Sequence Alignment Space-Efficient Sequence Alignment Bioinformatics 202 University of California, San Diego Lecture Notes No. 7 Dr. Pavel.

CAFE router: A Fast Connectivity Aware Multiple Nets Routing Algorithm for Routing Grid with Obstacles Y. Kohira and A. Takahashi School of Computer Science.

Simple Efficient Algorithm for MPQ-tree of an Interval Graph Toshiki SAITOH Masashi KIYOMI Ryuhei UEHARA Japan Advanced Institute of Science and Technology.

PROTEIN STRUCTURE NAME: ANUSHA. INTRODUCTION Frederick Sanger was awarded his first Nobel Prize for determining the amino acid sequence of insulin, the.

Graphs and DNA sequencing CS 466 Saurabh Sinha. Three problems in graph theory.

Pairwise Sequence Alignment (I) (Lecture for CS498-CXZ Algorithms in Bioinformatics) Sept. 22, 2005 ChengXiang Zhai Department of Computer Science University.

Random Generation and Enumeration of Bipartite Permutation Graphs Toshiki Saitoh (JAIST, Japan) Yota Otachi (Gunma Univ., Japan) Katsuhisa Yamanaka (UEC,

Graph Theory And Bioinformatics Jason Wengert. Outline Introduction to Graphs Eulerian Paths & Hamiltonian Cycles Interval Graph & Shape of Genes Sequencing.

Introduction to Graphs. Introduction Graphs are a generalization of trees –Nodes or verticies –Edges or arcs Two kinds of graphs –Directed –Undirected.

Flight Itinerary Problem ICS 311 Fall 2006 Matt Freeburg.

Dynamic Programming: Manhattan Tourist Problem Lecture 17.

Gene Prediction: Similarity-Based Methods (Lecture for CS498-CXZ Algorithms in Bioinformatics) Sept. 15, 2005 ChengXiang Zhai Department of Computer Science.

Some NP-complete Problems in Graph Theory Prof. Sin-Min Lee.

The Structure of the Web. Getting to knowing the Web How big is the web and how do you measure it? How many people use the web? How many use search engines?

Gene expression & Clustering. Determining gene function Sequence comparison tells us if a gene is similar to another gene, e.g., in a new species –Dynamic.

Randomized Algorithms Chapter 12 Jason Eric Johnson Presentation #3 CS Bioinformatics.

Pathfinding Algorithms for Mutating Weight Graphs Haitao Mao Computer Systems Lab

Introduction to Bioinformatics Algorithms Chapter 5 Greedy Algorithms and Genome Rearrangements By: Hasnaa Imad.

Network Partition –Finding modules of the network. Graph Clustering –Partition graphs according to the connectivity. –Nodes within a cluster is highly.

Dr Nazir A. Zafar Advanced Algorithms Analysis and Design Advanced Algorithms Analysis and Design By Dr. Nazir Ahmad Zafar.

Dynamic Programming (cont’d) CS 466 Saurabh Sinha.

Greedy Algorithms General principle of greedy algorithm

Sequence comparison: Local alignment

Introduction to Bioinformatics II

CS223 Advanced Data Structures and Algorithms

Intro to Alignment Algorithms: Global and Local

Clustering BE203: Functional Genomics Spring 2011 Vineet Bafna and Trey Ideker Trey Ideker Acknowledgements: Jones and Pevzner, An Introduction to Bioinformatics.

Graph Algorithms in Bioinformatics

Bioinformatics, Vol.17 Suppl.1 (ISMB 2001) Weekly Lab. Seminar

Greedy Algorithms Comp 122, Spring 2004.

Graphs G = (V, E) V are the vertices; E are the edges.

CSE 5290: Algorithms for Bioinformatics Fall 2009

Euler circuit Theorem 1 If a graph G has an Eulerian path, then it must have exactly two odd vertices. Theorem 2 If a graph G has an Eulerian circuit,

Algorithms Lecture # 27 Dr. Sohail Aslam.

Presentation transcript:

Splicing Exons: A Eukaryotic Challenge to Gene Prediction Ian McCoy

Gene Prediction Genes must be identified to make the genome useful Computational Problem: Take a seemingly random sequence of characters, millions or billions of bases long, and find the genes.

A Serious Complication Only 3% of the human genome contains genes

Similarity-Based Approach Instead of looking for a gene for a target protein directly, use a protein in a related organism. Find all local similarities between a genomic sequence and the target protein sequence. All substrings that exhibit a certain level of similarity will be called putative exons.

Exon-Chaining Problem 1. Use brute force to generate a set of putative exons. 2. Represent each exon with three parameters (l,r,w). 3. Find a maximum set of nonoverlapping putative exons.

Formulate as Graph Problem Create a graph G with 2n verticies: n vertices are starting(left) positions of exons and n vertices are ending(right) positions of exons. The set of left and right interval ends is sorted into increasing order. There are edges between each l i and r i of weight w i for I from 1 to n; and 2n-1 additional edges of weight 0 connecting adjacent vertices.

Input: A set of weighted intervals (putative exons) Output: The length of the maximum chain of intervals from this set

Dynamic Programming Algorithm ExonChaining (G, n) //Graph, number of intervals 1 for i ← 1 to 2n 2 s i ← 0 3 for i ← 2 to 2n 4 if vertex v i in G corresponds to right end of the interval I 5 j ← index of vertex for left end of the interval I 6 w ← weight of the interval I 7 s j ← max {s j + w, s i-1 } 8 else 9 s i ← s i-1 10 return s 2n

Shortcomings A large number of short exons will decrease the efficacy of our method for finding putative exons. Exons may be out of order.

Any Questions? Jones, Neil C., and Pavel A. Pevzner. An Introduction to Bioinformatics Algorithms. Cambridge: MIT Press, (p )