Estimating the Accuracy of Multiple Alignments and its Use in Parameter Advising

  • Dan F. DeBlasio
  • Travis J. Wheeler
  • John D. Kececioglu
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7262)


We develop a novel and general approach to estimating the accuracy of protein multiple sequence alignments without knowledge of a reference alignment, and use our approach to address a new problem that we call parameter advising. For protein alignments, we consider twelve independent features that contribute to a quality alignment. An accuracy estimator is learned that is a polynomial function of these features; its coefficients are determined by minimizing its error with respect to true accuracy using mathematical optimization. We evaluate this approach by applying it to the task of parameter advising: the problem of choosing alignment scoring parameters from a collection of parameter values to maximize the accuracy of a computed alignment. Our estimator, which we call Facet (for “feature-based accuracy estimator”), yields a parameter advisor that on the hardest benchmarks provides more than a 20% improvement in accuracy over the best default parameter choice, and outperforms the best prior approaches to selecting good alignments for parameter advising.


Integer Linear Program Structural Alignment Accuracy Estimator Parameter Choice Balance Weight 
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 2012

Authors and Affiliations

  • Dan F. DeBlasio
    • 1
  • Travis J. Wheeler
    • 2
  • John D. Kececioglu
    • 1
  1. 1.Department of Computer ScienceThe University of ArizonaUSA
  2. 2.Howard Hughes Medical InstituteUSA

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