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Computational Biology

Parameter Advising for Multiple Sequence Alignment

Authors: DeBlasio, Dan, Kececioglu, John D

  • 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
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eBook $84.99
price for USA in USD (gross)
  • ISBN 978-3-319-64918-4
  • Digitally watermarked, DRM-free
  • Included format: EPUB, PDF
  • ebooks can be used on all reading devices
  • Immediate eBook download after purchase
Hardcover $109.99
price for USA in USD
  • ISBN 978-3-319-64917-7
  • Free shipping for individuals worldwide
  • Usually dispatched within 3 to 5 business days.
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.

Table of contents (10 chapters)

  • Introduction and Background

    DeBlasio, Dan (et al.)

    Pages 1-15

  • Alignment Accuracy Estimation

    DeBlasio, Dan (et al.)

    Pages 19-27

  • The Facet Accuracy Estimator

    DeBlasio, Dan (et al.)

    Pages 29-40

  • Computational Complexity of Advising

    DeBlasio, Dan (et al.)

    Pages 41-49

  • Constructing Advisors

    DeBlasio, Dan (et al.)

    Pages 51-61

Buy this book

eBook $84.99
price for USA in USD (gross)
  • ISBN 978-3-319-64918-4
  • Digitally watermarked, DRM-free
  • Included format: EPUB, PDF
  • ebooks can be used on all reading devices
  • Immediate eBook download after purchase
Hardcover $109.99
price for USA in USD
  • ISBN 978-3-319-64917-7
  • Free shipping for individuals worldwide
  • Usually dispatched within 3 to 5 business days.
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Bibliographic Information

Bibliographic Information
Book Title
Parameter Advising for Multiple Sequence Alignment
Authors
Series Title
Computational Biology
Series Volume
26
Copyright
2017
Publisher
Springer International Publishing
Copyright Holder
Springer International Publishing AG
eBook ISBN
978-3-319-64918-4
DOI
10.1007/978-3-319-64918-4
Hardcover ISBN
978-3-319-64917-7
Series ISSN
1568-2684
Edition Number
1
Number of Pages
XIV, 152
Number of Illustrations and Tables
2 b/w illustrations, 30 illustrations in colour
Topics