Fast optimal genome tiling with applications to microarray design and homology search

Piotr Berman, Paul Bertone, Bhaskar DasGupta, Mark Gerstein, Ming Yang Kao, Michael Snyder

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    3 Citations (Scopus)

    Abstract

    In this paper we consider several variations of the following basic tiling problem: given a sequence of real numbers with two size bound parameters, we want to find a set of tiles such that they satisfy the size bounds and the total weight of the tiles is maximized. This solution to this problem is important to a number of computational biology applications, such as selecting genomic DNA fragments for amplicon microarrays, or performing homology searches with long sequence queries. Our goal is to design efficient algorithms with linear or near-linear time and space in the normal range of parameter values for these problems. For this purpose, we discuss the solution of a basic online interval maximum problem via a sliding window approach and show how to use this solution in a nontrivial manner for many of our tiling problems. We also discuss NPhardness and approximation algorithms for generalization of our basic tiling problem to higher dimensions.

    Original languageEnglish (US)
    Title of host publicationAlgorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings
    EditorsRoderic Guigo, Dan Gusfield
    PublisherSpringer Verlag
    Pages419-433
    Number of pages15
    ISBN (Print)3540442111, 9783540442110
    StatePublished - Jan 1 2002
    Event2nd International Workshop on Algorithms in Bioinformatics, WABI 2002 - Rome, Italy
    Duration: Sep 17 2002Sep 21 2002

    Publication series

    NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
    Volume2452
    ISSN (Print)0302-9743
    ISSN (Electronic)1611-3349

    Other

    Other2nd International Workshop on Algorithms in Bioinformatics, WABI 2002
    CountryItaly
    CityRome
    Period9/17/029/21/02

    Fingerprint

    Microarrays
    Tile
    Tiling
    Microarray
    Homology
    Genome
    Genes
    Approximation algorithms
    DNA
    Sliding Window
    Computational Biology
    Linear Space
    Higher Dimensions
    Genomics
    Design
    Linear Time
    Approximation Algorithms
    Fragment
    Efficient Algorithms
    Query

    All Science Journal Classification (ASJC) codes

    • Theoretical Computer Science
    • Computer Science(all)

    Cite this

    Berman, P., Bertone, P., DasGupta, B., Gerstein, M., Kao, M. Y., & Snyder, M. (2002). Fast optimal genome tiling with applications to microarray design and homology search. In R. Guigo, & D. Gusfield (Eds.), Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings (pp. 419-433). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 2452). Springer Verlag.
    Berman, Piotr ; Bertone, Paul ; DasGupta, Bhaskar ; Gerstein, Mark ; Kao, Ming Yang ; Snyder, Michael. / Fast optimal genome tiling with applications to microarray design and homology search. Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings. editor / Roderic Guigo ; Dan Gusfield. Springer Verlag, 2002. pp. 419-433 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
    @inproceedings{b09ac031d1f64c4fbf6d998097b7e6fd,
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    abstract = "In this paper we consider several variations of the following basic tiling problem: given a sequence of real numbers with two size bound parameters, we want to find a set of tiles such that they satisfy the size bounds and the total weight of the tiles is maximized. This solution to this problem is important to a number of computational biology applications, such as selecting genomic DNA fragments for amplicon microarrays, or performing homology searches with long sequence queries. Our goal is to design efficient algorithms with linear or near-linear time and space in the normal range of parameter values for these problems. For this purpose, we discuss the solution of a basic online interval maximum problem via a sliding window approach and show how to use this solution in a nontrivial manner for many of our tiling problems. We also discuss NPhardness and approximation algorithms for generalization of our basic tiling problem to higher dimensions.",
    author = "Piotr Berman and Paul Bertone and Bhaskar DasGupta and Mark Gerstein and Kao, {Ming Yang} and Michael Snyder",
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    Berman, P, Bertone, P, DasGupta, B, Gerstein, M, Kao, MY & Snyder, M 2002, Fast optimal genome tiling with applications to microarray design and homology search. in R Guigo & D Gusfield (eds), Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 2452, Springer Verlag, pp. 419-433, 2nd International Workshop on Algorithms in Bioinformatics, WABI 2002, Rome, Italy, 9/17/02.

    Fast optimal genome tiling with applications to microarray design and homology search. / Berman, Piotr; Bertone, Paul; DasGupta, Bhaskar; Gerstein, Mark; Kao, Ming Yang; Snyder, Michael.

    Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings. ed. / Roderic Guigo; Dan Gusfield. Springer Verlag, 2002. p. 419-433 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 2452).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

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    AU - Berman, Piotr

    AU - Bertone, Paul

    AU - DasGupta, Bhaskar

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    AU - Kao, Ming Yang

    AU - Snyder, Michael

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    AB - In this paper we consider several variations of the following basic tiling problem: given a sequence of real numbers with two size bound parameters, we want to find a set of tiles such that they satisfy the size bounds and the total weight of the tiles is maximized. This solution to this problem is important to a number of computational biology applications, such as selecting genomic DNA fragments for amplicon microarrays, or performing homology searches with long sequence queries. Our goal is to design efficient algorithms with linear or near-linear time and space in the normal range of parameter values for these problems. For this purpose, we discuss the solution of a basic online interval maximum problem via a sliding window approach and show how to use this solution in a nontrivial manner for many of our tiling problems. We also discuss NPhardness and approximation algorithms for generalization of our basic tiling problem to higher dimensions.

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    T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

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    BT - Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings

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    Berman P, Bertone P, DasGupta B, Gerstein M, Kao MY, Snyder M. Fast optimal genome tiling with applications to microarray design and homology search. In Guigo R, Gusfield D, editors, Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings. Springer Verlag. 2002. p. 419-433. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).