'Suffix array' presentation slideshows

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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Short Read Mapping On Post Genomics Datasets

Short Read Mapping On Post Genomics Datasets. Adapted from Langmead Trapnell, Pop, Salzberg. Cedric Notredame. DATA. The Data: FASTQ. The Data: CSFASTQ (ABI). Data SAM. The Data: BAM. The Data: SAM/BAM. SAM/BAM Tools. SAM/BAM: Visualization. SAM/BAM: Visualization. SHORT READS.

970 views • 75 slides

LINGO

LINGO. Search Results Clustering. Sandra Gama. Internet ? endless document collection . Search Engines. NO question answering. FAST access to Web content. SENSITIVE to query quality. we NEED meaningful RESULTS. CLUSTERING!. GROUPING by Similarity. Semantic structure. Groups.

866 views • 61 slides

Hamsa: Fast Signature Generation for Zero-day Polymorphic Worms with Provable Attack Resilience

Hamsa: Fast Signature Generation for Zero-day Polymorphic Worms with Provable Attack Resilience. Lab for Internet & Security Technology (LIST) Northwestern University. The Spread of Sapphire/Slammer Worms. Desired Requirements for Polymorphic Worm Signature Generation.

772 views • 61 slides

Linear-Time Search in Suffix Arrays

July 14, 2003 Jeong Seop Sim, Dong Kyue Kim Heejin Park, Kunsoo Park. Linear-Time Search in Suffix Arrays. Suffix arrays. Suffix array of text T The lexicographically sorted list of all suffixes of text T. Suffix arrays. Example for T = abbabaababbb#

613 views • 43 slides

Text Indexing

Text Indexing. S. Srinivasa Rao April 19, 2007 [based on slides by Paolo Ferragina]. Why string data are interesting ?. They are ubiquitous: Digital libraries and product catalogues Electronic white and yellow pages Specialized information sources (e.g. Genomic or Patent dbs)

552 views • 41 slides

Suffix Trees and Suffix Arrays

Suffix Trees and Suffix Arrays. Some problems. Given a pattern P = P[1..m], find all occurrences of P in a text S = S[1..n] Another problem: Given two strings S 1 [1..n 1 ] and S 2 [1..n 2 ] find their longest common substring.

596 views • 38 slides

Suffix Trees and Suffix Arrays

Suffix Trees and Suffix Arrays. Some problems. Given a pattern P = P[1..m], find all occurrences of P in a text S = S[1..n] Another problem: Given two strings S 1 [1..n 1 ] and S 2 [1..n 2 ] find their longest common substring.

626 views • 38 slides

Next Generation Sequencing, Assembly, and Alignment Methods

Next Generation Sequencing, Assembly, and Alignment Methods . Andy Nagar. Agenda. Background Next Generation Sequencing Sequence Assembly Sequence Alignment Traditional Alignment Algorithms Next Generation Alignment Algorithms Conclusion. Background.

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Indexing and Searching

Indexing and Searching. Modern Information Retrieval by R. Baeza-Yates and B. Ribeiro-Neto Chapter 8. Outline. Inverted Files Other Indices for Text Sequential Searching Pattern Matching Compression. Inverted Files.

643 views • 32 slides

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??????. ????? , ?????? ????? , ???????. Overview of Key Techniques in IR. Prof. Xiaoyong Du. Core Techniques. Metadata-level Techniques. Indexing. Search. Compression. Media-Related Interpretation. Text Operator. image operator. Video operator. Unstructured data.

470 views • 30 slides

Simple Linear Work Suffix Array Construction

468 views • 29 slides

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.

372 views • 27 slides

Counting Suffix Arrays and Strings

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Parallel Suffix Array Construction by Accelerated Sampling

Parallel Suffix Array Construction by Accelerated Sampling. Matthew Felice Pace University of Warwick. Joint work with Alexander Tiskin University of Warwick. Outline. Introduction Difference Covers Sequential Suffix Array Construction Bulk-Synchronous Parallel (BSP) Model

337 views • 21 slides

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

296 views • 17 slides

q-gram Based Database Searching Using A Suffix Array (QUASAR)

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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?.

350 views • 14 slides

Kunihiko Sadakane Department of Information Science University of Tokyo

A Modified Burrows-Wheeler Transformation for Case-insensitive Search with Application to Suffix Array Compression. Kunihiko Sadakane Department of Information Science University of Tokyo. faster than PPMs decoding is much faster comparable performance with PPMs. search data structure

224 views • 11 slides

119 views • 8 slides