© 2017

Parameter Advising for Multiple Sequence Alignment


  • Presents practical approaches to the pervasive question of how to choose parameter settings for sequence alignment

  • Provides links to proven software implementations that work well on real data

  • Introduces a general framework for parameter advising of broad utility in bioinformatics and beyond


Part of the Computational Biology book series (COBO, volume 26)

Table of contents

  1. Front Matter
    Pages i-xiv
  2. Dan DeBlasio, John Kececioglu
    Pages 1-15
  3. Foundations of Parameter Advising

    1. Front Matter
      Pages 17-17
    2. Dan DeBlasio, John Kececioglu
      Pages 19-27
    3. Dan DeBlasio, John Kececioglu
      Pages 29-40
    4. Dan DeBlasio, John Kececioglu
      Pages 41-49
    5. Dan DeBlasio, John Kececioglu
      Pages 51-61
  4. Applications of Parameter Advising

    1. Front Matter
      Pages 63-63
    2. Dan DeBlasio, John Kececioglu
      Pages 65-83
    3. Dan DeBlasio, John Kececioglu
      Pages 85-102
    4. Dan DeBlasio, John Kececioglu
      Pages 103-115
    5. Dan DeBlasio, John Kececioglu
      Pages 117-137
    6. Dan DeBlasio, John Kececioglu
      Pages 139-142
  5. Back Matter
    Pages 143-152

About this book


This book develops a new approach called parameter advising for finding a parameter setting for a sequence aligner that yields a quality alignment of a given set of input sequences. In this framework, a parameter advisor is a procedure that automatically chooses a parameter setting for the input, and has two main ingredients:

(a)         the set of parameter choices considered by the advisor, and

(b)         an estimator of alignment accuracy used to rank alignments produced by the aligner.

On coupling a parameter advisor with an aligner, once the advisor is trained in a learning phase, the user simply inputs sequences to align, and receives an output alignment from the aligner, where the advisor has automatically selected the parameter setting.

The chapters first lay out the foundations of parameter advising, and then cover applications and extensions of advising. The content

•   examines formulations of parameter advising and their computational complexity,

•   develops methods for learning good accuracy estimators,

•   presents approximation algorithms for finding good sets of parameter choices, and

•   assesses software implementations of advising that perform well on real biological data.

Also explored are applications of parameter advising to

•   adaptive local realignment, where advising is performed on local regions of the sequences to automatically adapt to varying mutation rates, and

•   ensemble alignment, where advising is applied to an ensemble of aligners to effectively yield a new aligner of higher quality than the individual aligners in the ensemble.

The book concludes by offering future directions in advising research.


Bioinformatics Biological sequence analysis Multiple sequence alignment Protein sequence alignment Alignment accuracy Alignment scoring parameters Substitution matrices Gap penalties Refining alignments Machine learning Ensemble methods Computational complexity Approximation algorithms Linear programming Integer linear programming

Authors and affiliations

  1. 1.Computational Biology DepartmentCarnegie Mellon UniversityPittsburghUSA
  2. 2.Department of Computer ScienceThe University of ArizonaTucsonUSA

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