'Suffix arrays' diaporamas de présentation

Contents

Contents. First week : algorithms for exact string matching: One pattern : The algorithm depends on |p| and | ?? k patterns : The algorithm depends on k, |p| and | ? | Second week : Alignment of sequences. Edit distance between two strings: dynamic programming Alignment of sequences:

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Compressed Suffix Arrays

Compressed Suffix Arrays. Compression of Suffix Arrays to linear size. Fabian Pache. Motivation. Problem: Suffix Arrays are datastructures that support fast searching of patterns in long texts, but require large amounts of memory

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A Lempel-Ziv text index on secondary storage

Combinatorial Pattern Matching 2007. A Lempel-Ziv text index on secondary storage. Diego Arroyuelo and Gonzalo Navarro. Index. T. P. P. P. P. Introduction. The full-text searching problem :

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Sequence Clustering

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Motive

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Wie oft matcht das Profil ?

Wie oft matcht das Profil ?. T A T A C G A A T C T A A A. Wie oft matcht das Profil ?. 1. 2. 3. 4. T A T A C G A A T C T A A A. Suche nach Motiven mit PSSMs und Enhanced Suffix Array.

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Counting Suffix Arrays and Strings

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A Categorization Theorem on Suffix Arrays with Applications to Space Efficient Text Indexes

A Categorization Theorem on Suffix Arrays with Applications to Space Efficient Text Indexes. Meng He, J. Ian Munro, and S. Srinivasa Rao University of Waterloo. The Problem. Initial Problem Text searching : Finding occurrences of a pattern string in a large (static) document Solution

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Suffix Array: Data structures and applications

Suffix Array: Data structures and applications. Zhifeng Liu School of Computer Science, Univ. of Waterloo Dec. 06, 2004. Outline. Introduction Suffix array and enhanced suffix array An example - Is P a substring of S ? Conclusions References. Introduction Why suffix array?.

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Succinct Data Structures

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Succinct Data Structures

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Midterm Review

Midterm Review. Review of previous weeks. Pairwise sequence alignment Scoring matrices PAM, BLOSUM, Dynamic programming Needleman-Wunsch (Global) Semi-global (no end-gap penalties) Smith-Waterman (Local). Review of previous weeks. Statistical significance of alignments

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