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Phylogenetic Footprinting and Consistent Sets of Local Aligments

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Combinatorial Pattern Matching (CPM 2011)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 6661))

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Abstract

The problem of constructing alternative local multiple sequence alignments from a collection of local pairwise alignments arises naturally in phylogenetic footprinting, a technique used to identify regulatory elements by comparative sequence analysis. Based on a theoretical discussion of the problem we devise an efficient heuristic and introduce the software tool tracker2 for this task. Tests on both biological and random data demonstrated the heuristic yields excellent results at very short runtimes.

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References

  1. Elnitski, L., Jin, V.X., Farnham, P.J., Jones, S.J.M.: Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques. Genome Res. 16, 1455–1464 (2006)

    Article  Google Scholar 

  2. Bailey, T.L., Williams, N., Misleh, C., Li, W.W.: MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 34, W369–W373 (2006)

    Article  Google Scholar 

  3. Blanchette, M., Tompa, M.: Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res. 12, 739–748 (2002)

    Article  Google Scholar 

  4. Liu, Y., Liu, X., Wei, L., Altman, R., Batzoglou, S.: Eukaryotic regulatory element conservation analysis and identification using comparative genomics. Genome Res. 14, 451–458 (2004)

    Article  Google Scholar 

  5. Siddharthan, R., Siggia, E., van Nimwegen, E.: PhyloGibbs: A gibbs sampling motif finder that incorporates phylogeny. PLoS Comput. Biol. 1, e67 (2005)

    Article  Google Scholar 

  6. van Nimwegen, E.: Finding regulatory elements and regulatory motifs: a general probabilistic framework. BMC Bioinformatics 8 (suppl. 6), S4 (2007)

    Article  Google Scholar 

  7. Gordân, R., Narlikar, L., Hartemink, A.J.: Finding regulatory DNA motifs using alignment-free evolutionary conservation information. Nucleic Acids Res. 38, e90 (2010)

    Article  Google Scholar 

  8. Margulies, E.H., Blanchette, M., Haussler, D., Green, E.D.: Identification and characterization of multi-species conserved sequences. Genome Res. 13, 2507–2518 (2003)

    Article  Google Scholar 

  9. Zhang, Z., Gerstein, M.: Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements. J. Biol. 2, 11 (2003)

    Article  Google Scholar 

  10. Prohaska, S., Fried, C., Flamm, C., Wagner, G., Stadler, P.F.: Surveying phylogenetic footprints in large gene clusters: Applications to Hox cluster duplications. Mol. Phyl. Evol. 31, 581–604 (2004)

    Article  Google Scholar 

  11. Morgenstern, B., Stoye, J., Dress, A.W.M.: Consistent equivalence relations: a set-theoretical framework for multiple sequence alignments. Technical report, University of Bielefeld, FSPM (1999)

    Google Scholar 

  12. Corel, E., Pitschi, F., Morgenstern, B.: A min-cut algorithm for the consistency problem in multiple sequence alignment. Bioinformatics 26, 1015–1021 (2010)

    Article  Google Scholar 

  13. Morgenstern, B., Frech, K., Dress, A., Werner, T.: DIALIGN: finding local similarities by multiple sequence alignment. Bioinformatics 14(3), 290–294 (1998)

    Article  Google Scholar 

  14. Tarjan, R.E.: Depth first search and linear graph algorithms. SIAM J. Computing 1, 146–160 (1972)

    Article  MathSciNet  MATH  Google Scholar 

  15. Notredame, C., Higgins, D.G., Heringa, J.: T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205–217 (2000)

    Article  Google Scholar 

  16. Euler, R.: On a classification of independence systems. Math. Methods Operations Res. 27, 123–136 (1983)

    Article  MathSciNet  MATH  Google Scholar 

  17. Helman, P., Moret, B.M.E., Shapiro, H.D.: An exact characterization of greedy structures. SIAM J. Discrete Math. 6, 274–283 (1993)

    Article  MathSciNet  MATH  Google Scholar 

  18. Elias, I.: Settling the intractability of multiple alignment. J. Comp. Biol. 13, 1323–1339 (2006)

    Article  MathSciNet  Google Scholar 

  19. Wilm, A., Mainz, I., Steger, G.: An enhanced RNA alignment benchmark for sequence alignment programs. Algorithms Mol. Biol. 1, 19 (2006)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103, Leipzig, Germany

    Wolfgang Otto & Peter F. Stadler

  2. Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany

    Wolfgang Otto, Peter F. Stadler & Sonja J. Prohaska

  3. Computational EvoDevo Group, Department of Computer Science, University of Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany

    Sonja J. Prohaska

  4. Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany

    Peter F. Stadler

  5. Fraunhofer Institut für Zelltherapie und Immunologie, Perlickstraße 1, D-04103, Leipzig, Germany

    Peter F. Stadler

  6. Center for noncoding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, DK-1870, Frederiksberg C, Denmark

    Peter F. Stadler

  7. Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090, Wien, Austria

    Peter F. Stadler

  8. Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA

    Peter F. Stadler

Authors
  1. Wolfgang Otto
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  2. Peter F. Stadler
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  3. Sonja J. Prohaska
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Editor information

Editors and Affiliations

  1. Department of Mathematics, Università degli Studi di Palermo, Via Archirafi 34, 90123, Palermo, Italy

    Raffaele Giancarlo

  2. Department of Computer Science, University of ’Piemonte Orientale’, Viale T. Michel 11, 15121, Alessandria, Italy

    Giovanni Manzini

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© 2011 Springer-Verlag Berlin Heidelberg

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Otto, W., Stadler, P.F., Prohaska, S.J. (2011). Phylogenetic Footprinting and Consistent Sets of Local Aligments. In: Giancarlo, R., Manzini, G. (eds) Combinatorial Pattern Matching. CPM 2011. Lecture Notes in Computer Science, vol 6661. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21458-5_12

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  • DOI: https://doi.org/10.1007/978-3-642-21458-5_12

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-21457-8

  • Online ISBN: 978-3-642-21458-5

  • eBook Packages: Computer ScienceComputer Science (R0)

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