'Suffix tree' presentation slideshows

Suffix trees

Suffix trees. Trie. A tree representing a set of strings. c. a. { aeef ad bbfe bbfg c }. b. e. b. d. e. f. c. f. e. g. Trie (Cont). Assume no string is a prefix of another. c. Each edge is labeled by a letter,

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Algorithms in Bioinformatics: A Practical Introduction

Algorithms in Bioinformatics: A Practical Introduction. Suffix tree. Overview. What is suffix tree? Simple application of suffix tree Linear time algorithm for constructing suffix tree Suffix array FM-index 1-mismatch search. Suffix. 1. acacag$. 2. cacag$. 3. acag$. 4. cag$. 5.

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Suffix tree and suffix array techniques for pattern analysis in strings

Suffix tree and suffix array techniques for pattern analysis in strings. Esko Ukkonen Univ Helsinki Erice School 30 Oct 2005.

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Suffix Trees

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Microarray - Introduction

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CS5263 Bioinformatics

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Applications

Applications. Exact string and substring matching Longest common substrings Finding and representing repeated substrings efficiently Applications that lead to alternative, space efficient implementations Matching statistics Suffix Arrays. String and substrings. Exact String matching:

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Speaker: C. C. Lin Adviser: R. C. T. Lee

String Matching with k Mismatches by Using Kangaroo Method Efficient string with k mismatches, Landau, G.M., and Vishkin, U., Theoret. Comput Sci 43, 1986, pp. 239-249. Speaker: C. C. Lin Adviser: R. C. T. Lee. Problem definition: Input: A text T with length n , a pattern P with

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Suffix Trees Come of Age in Bioinformatics

Suffix Trees Come of Age in Bioinformatics. Algorithms, Applications and Implementations Dan Gusfield, U.C. Davis. 1 2 3 4 5 6. AABAAB. S =. Suffix Tree. B. A. A. A. B. $. B. A. 3. $. $. B. A. 5. 6. A. $. 4. B. A. $. A. 2. B.

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Inferring Strings from Suffix Trees and Links on a Binary Alphabet

Inferring Strings from Suffix Trees and Links on a Binary Alphabet. Tomohiro I , Shunsuke Inenaga , Hideo Bannai , Masayuki Takeda Kyushu University, Japan. Outline. Reverse Problems on String Data Structures Suffix Tree, Suffix Links Reverse Problem on Suffix Trees Efficient Solution

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CS 182 Sections 103 - 104

CS 182 Sections 103 - 104. slides created by Eva Mok ( emok@icsi.berkeley.edu ) modified by JGM March 22, 2006. The Last Stretch. Psycholinguistics Experiments. Spatial Relation. Motor Control. Metaphor. Grammar. Cognition and Language. Computation. Chang Model. Bailey Model.

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Large-Scale Global Alignments Multiple Alignments

Large-Scale Global Alignments Multiple Alignments. Lecture 10, Thursday May 1, 2003. ARACHNE: Steps to Assemble a Genome. 1. Find overlapping reads. 2. Merge good pairs of reads into longer contigs. 3. Link contigs to form supercontigs. 4. Derive consensus sequence.

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Motivation

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Suffix Trees

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AC-Suffix-Tree ? Buffer Free String Matching on Out-of-Sequence Packets

AC-Suffix-Tree ? Buffer Free String Matching on Out-of-Sequence Packets. Author ? Xinming Chen ,Kailin Ge ,Zhen Chen and Jun Li Publisher ? ANCS , 2011 Presenter ? Tsung-Lin Hsieh Date ? 2011/12/14. Outline . Introduction Related Work Background

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Fast Exact String Matching On the GPU

Fast Exact String Matching On the GPU. Michael C. Schatz and Cole Trapnell May 8, 2007 CMSC 740 Computer Graphics. String Matching Applications. A very common problem in computational biology is to find all occurrences (or approximate occurrences) of one string in another string

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Created by: Yung-Hsing Peng Date: Sep. 17, 2004

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My Beats

My Beats. Karen Tipping Dylan Barrett Mike Smith. Overview. Goal: To dynamically create tracks for guitar hero using any song as input. Terminology for our project Song Track Button Segment. Technology. Frets on Fire (FoF) ? Analyze by The Echo Nest Java.

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Information Retrieval Homework #1

Information Retrieval Homework #1. Members: Wesley, Lbr, Shuang CSIE, NCU. Outline. Introduction Stemming Algorithm Suffix Tree Performance Conclusion. Stemming Algorithm (optional). Goal of stemming improve performance and require less resources by reducing the number of unique words

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