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Parametric recomputing in alignment graphs

  • Xiaoqiu Huang
  • Pavel A. Pevzner
  • Webb Miller
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 807)

Abstract

DNA/protein sequence alignments in computational molecular biology depend heavily on the settings of penalties for substitutions, insertions/deletions and gaps. Inappropriate choice of parameters causes irrelevant matches (“noise”) to be reported, thus obscuring biologically relevant matches. In practice, biologists frequently compare sequences in a few iterations, starting from a vague idea about appropriate parameters, then refining parameters to reduce noise. This procedure often helps to delineate biologically interesting similarities and to substantially reduce laborious analysis. This paper provides a computational underpinning for such iterative noise filtration in alignment graphs. Our main results assume that a preliminary “noisy” alignment, computed with reasonable but ad hoc parameters, is given; the problem is to modify the parameters to reduce noise. We present fast algorithms to refine penalty parameters and describe an application of these algorithms.

Keywords

Decomposition Tree Optimal Alignment Locus Control Region Alignment Graph Computational Molecular Biology 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 1994

Authors and Affiliations

  • Xiaoqiu Huang
    • 1
  • Pavel A. Pevzner
    • 2
  • Webb Miller
    • 2
  1. 1.Department of Computer ScienceMichigan Technological UniversityHoughton
  2. 2.Computer Science DepartmentThe Pennsylvania State UniversityUniversity Park

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