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Phylogenetic Footprinting and Consistent Sets of Local Aligments

  • Wolfgang Otto
  • Peter F. Stadler
  • Sonja J. Prohaska
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6661)

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.

Keywords

alignment consistency phylogenetic footprinting combinatorial optimization tracker2 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Wolfgang Otto
    • 1
    • 2
  • Peter F. Stadler
    • 1
    • 2
    • 4
    • 5
    • 6
    • 7
    • 8
  • Sonja J. Prohaska
    • 3
    • 2
  1. 1.Max Planck Institute for Mathematics in the SciencesLeipzigGermany
  2. 2.Interdisciplinary Center for BioinformaticsUniversity of LeipzigLeipzigGermany
  3. 3.Computational EvoDevo Group, Department of Computer ScienceUniversity of LeipzigLeipzigGermany
  4. 4.Bioinformatics Group, Department of Computer ScienceUniversity of LeipzigLeipzigGermany
  5. 5.Fraunhofer Institut für Zelltherapie und ImmunologieLeipzigGermany
  6. 6.Center for noncoding RNA in Technology and HealthUniversity of CopenhagenFrederiksberg CDenmark
  7. 7.Department of Theoretical ChemistryUniversity of ViennaWienAustria
  8. 8.Santa Fe InstituteSanta FeUSA

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