Repository logo

Infoscience

  • English
  • French
Log In
Logo EPFL, École polytechnique fédérale de Lausanne

Infoscience

  • English
  • French
Log In
  1. Home
  2. Academic and Research Output
  3. Journal articles
  4. Sorting signed permutations by inversions in O(nlogn) time
 
research article

Sorting signed permutations by inversions in O(nlogn) time

Swenson, K. M.  
•
Rajan, V.
•
Lin, Y.  
Show more
2010
Journal of Computational Biology

The study of genomic inversions (or reversals) has been a mainstay of computational genomics for nearly 20 years. After the initial breakthrough of Hannenhalli and Pevzner, who gave the first polynomial-time algorithm for sorting signed permutations by inversions, improved algorithms have been designed, culminating with an optimal linear-time algorithm for computing the inversion distance and a subquadratic algorithm for providing a shortest sequence of inversions-also known as sorting by inversions. Remaining open was the question of whether sorting by inversions could be done in O(nlogn) time. In this article, we present a qualified answer to this question, by providing two new sorting algorithms, a simple and fast randomized algorithm and a deterministic refinement. The deterministic algorithm runs in time O(nlogn + kn), where k is a data-dependent parameter. We provide the results of extensive experiments showing that both the average and the standard deviation for k are small constants, independent of the size of the permutation. We conclude (but do not prove) that almost all signed permutations can be sorted by inversions in O(nlogn) time.

  • Details
  • Metrics
Type
research article
DOI
10.1089/cmb.2009.0184
Web of Science ID

WOS:000279271600020

Author(s)
Swenson, K. M.  
Rajan, V.
Lin, Y.  
Moret, B. M. E.  
Date Issued

2010

Published in
Journal of Computational Biology
Volume

17

Issue

3

Start page

489

End page

501

Subjects

algorithms

•

combinatorics

•

computational molecular biology

•

genomic rearrangements

•

phylogenetic trees

•

Reversals

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
LCBB  
Available on Infoscience
March 12, 2010
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/48053
Logo EPFL, École polytechnique fédérale de Lausanne
  • Contact
  • infoscience@epfl.ch

  • Follow us on Facebook
  • Follow us on Instagram
  • Follow us on LinkedIn
  • Follow us on X
  • Follow us on Youtube
AccessibilityLegal noticePrivacy policyCookie settingsEnd User AgreementGet helpFeedback

Infoscience is a service managed and provided by the Library and IT Services of EPFL. © EPFL, tous droits réservés