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  1. No Access

    Chapter

    A Computational Approach to Search for Non-Coding RNAs in Large Genomic Data

    Over the last few years several specialized software tools have been developed, each allowing a certain class of RNAs insequencedatatobe found.Herewedescribeageneral tool that allows us to specify many differe...

    Stefan Gräf, Jan-Hendrik Teune, Dirk Strothmann, Stefan Kurtz, Gerhard Steger in Small RNAs (2006)

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    Chapter and Conference Paper

    Optimal Exact String Matching Based on Suffix Arrays

    Using the suffix tree of a string S, decision queries of the type “Is P a substring of S?” can be answered in O(|P|) time and enumeration queries of the type “Where are all z occurrences of P in S?” can be answer...

    Mohamed Ibrahim Abouelhoda, Enno Ohlebusch… in String Processing and Information Retrieval (2002)

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    Chapter and Conference Paper

    The Enhanced Suffix Array and Its Applications to Genome Analysis

    In large scale applications as computational genome analysis, the space requirement of the suffix tree is a severe drawback. In this paper, we present a uniform framework that enables us to systematically repl...

    Mohamed Ibrahim Abouelhoda, Stefan Kurtz, Enno Ohlebusch in Algorithms in Bioinformatics (2002)

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    Chapter

    Space Efficient Linear Time Computation of the Burrows and Wheeler-Transformation

    In [4] a universal data compression algorithm (BW-algorithm, for short) is described which achieves compression rates that are close to the best known rates achieved in practice. Due to its simplicity, the alg...

    Stefan Kurtz, Bernhard Balkenhol in Numbers, Information and Complexity (2000)

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    Chapter and Conference Paper

    Efficient Implementation of Lazy Suffix Trees

    We present an efficient implementation of a write-only topdown construction for suffix trees. Our implementation is based on a new, space-efficient representation of suffix trees which requires only 12 bytes p...

    Robert Giegerich, Stefan Kurtz, Jens Stoye in Algorithm Engineering (1999)

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    Chapter and Conference Paper

    Estimating the probability of approximate matches

    Stefan Kurtz, Gene Myers in Combinatorial Pattern Matching (1997)

  7. Chapter and Conference Paper

    Suffix trees in the functioned programming paradigm

    We explore the design space of implementing suffix tree algorithms in the functional paradigm. We review the linear time and space algorithms of McCreight and Ukkonen. Based on a new terminology of nested suff...

    Robert Giegerich, Stefan Kurtz in Programming Languages and Systems — ESOP '94 (1994)

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