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Efficient Extraction of Structured Motifs Using Box-Links

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String Processing and Information Retrieval (SPIRE 2004)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 3246))

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Abstract

In this paper we propose a new data structure for the efficient extraction of structured motifs from DNA sequences. A structured motif is defined as a collection of highly conserved motifs with pre-specified sizes and spacings between them. The new data structure, called box-link, stores the information on how to jump over the spacings which separate each motif in a structured motif. A factor tree, a variation of a suffix tree, endowed with box-links provide the means for the efficient extraction of structured motifs.

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References

  1. Marsan, L., Sagot, M.F.: Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification. J. Comp. Bio. 7, 345–362 (2000)

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  2. Sharan, R., Ovcharenko, I., Ben-Hur, A., Karp, R.M.: Creme: a framework for identifying cis-regulatory modules in human-mouse conserved segments. Bioinformatics 19, i283–i291 (2003)

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  3. Segal, E., Barash, Y., Simon, I., Friedman, N., Koller, D.: A discriminative model for identifying spatial cis-regulatory modules. In: Proc. RECOMB 2004, pp. 141–149 (2004)

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  4. Allali, J., Sagot, M.F.: The at most k-deep factor tree. Submitted for publication (2003)

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Author information

Authors and Affiliations

  1. IST/INESC-ID, Rua Alves Redol, 9, 1000-029, Lisboa, Portugal

    Alexandra M. Carvalho, Ana T. Freitas & Arlindo L. Oliveira

  2. Inria Rhône-Alpes, Université Claude Bernard, Lyon I, 43 Bd du 11 Novembre 1918, 69622, Villeurbanne Cedex, France

    Marie-France Sagot

Authors
  1. Alexandra M. Carvalho
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  2. Ana T. Freitas
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  3. Arlindo L. Oliveira
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  4. Marie-France Sagot
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Editor information

Editors and Affiliations

  1. Georgia Institute of Technology and Università di Padova,  

    Alberto Apostolico

  2. Department of Information Engineering, University of Padova,  

    Massimo Melucci

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© 2004 Springer-Verlag Berlin Heidelberg

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Carvalho, A.M., Freitas, A.T., Oliveira, A.L., Sagot, MF. (2004). Efficient Extraction of Structured Motifs Using Box-Links. In: Apostolico, A., Melucci, M. (eds) String Processing and Information Retrieval. SPIRE 2004. Lecture Notes in Computer Science, vol 3246. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30213-1_37

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  • DOI: https://doi.org/10.1007/978-3-540-30213-1_37

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-23210-0

  • Online ISBN: 978-3-540-30213-1

  • eBook Packages: Springer Book Archive

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