Skip Navigation


Bioinformatics Advance Access originally published online on June 9, 2005
Bioinformatics 2005 21(16):3340-3346; doi:10.1093/bioinformatics/bti535
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
21/16/3340    most recent
bti535v2
bti535v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (20)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Yancopoulos, S.
Right arrow Articles by Friedberg, R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Yancopoulos, S.
Right arrow Articles by Friedberg, R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Efficient sorting of genomic permutations by translocation, inversion and block interchange

Sophia Yancopoulos 1,*, Oliver Attie 2 and Richard Friedberg 3

1The Feinstein Institute for Medical Research North Shore-LIJ Health System, Manhasset, NY 11030, USA
2Center for the Study of Gene Structure and Function, Hunter College NY, NY 10021, USA
3Department of Physics, Columbia University NY, NY 10027, USA

*To whom correspondence should be addressed.

Motivation: Finding genomic distance based on gene order is a classic problem in genome rearrangements. Efficient exact algorithms for genomic distances based on inversions and/or translocations have been found but are complicated by special cases, rare in simulations and empirical data. We seek a universal operation underlying a more inclusive set of evolutionary operations and yielding a tractable genomic distance with simple mathematical form.

Results: We study a universal double-cut-and-join operation that accounts for inversions, translocations, fissions and fusions, but also produces circular intermediates which can be reabsorbed. The genomic distance, computable in linear time, is given by the number of breakpoints minus the number of cycles (b–c) in the comparison graph of the two genomes; the number of hurdles does not enter into it. Without changing the formula, we can replace generation and re-absorption of a circular intermediate by a generalized transposition, equivalent to a block interchange, with weight two. Our simple algorithm converts one multi-linear chromosome genome to another in the minimum distance.

Contact: syancopo{at}nshs.edu

Received on May 3, 2005; revised on June 2, 2005; accepted on June 8, 2005

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Genome ResHome page
H. Zhao and G. Bourque
Recovering genome rearrangements in the mammalian phylogeny
Genome Res., May 1, 2009; 19(5): 934 - 942.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
M. A. Alekseyev and P. A. Pevzner
Breakpoint graphs and ancestral genome reconstructions
Genome Res., May 1, 2009; 19(5): 943 - 957.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
B. Paten, J. Herrero, K. Beal, S. Fitzgerald, and E. Birney
Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
Genome Res., November 1, 2008; 18(11): 1814 - 1828.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. Ma, A. Ratan, B. J. Raney, B. B. Suh, W. Miller, and D. Haussler
Inaugural Article: The infinite sites model of genome evolution
PNAS, September 23, 2008; 105(38): 14254 - 14261.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
C. Zheng, Q. Zhu, Z. Adam, and D. Sankoff
Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes
Bioinformatics, July 1, 2008; 24(13): i96 - i104.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Y. Lin and B. M.E. Moret
Estimating true evolutionary distances under the DCJ model
Bioinformatics, July 1, 2008; 24(13): i114 - i122.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. Gog, M. Bader, and E. Ohlebusch
GENESIS: genome evolution scenarios
Bioinformatics, March 1, 2008; 24(5): 711 - 712.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y. C. Lin, C. L. Lu, Y.-C. Liu, and C. Y. Tang
SPRING: a tool for the analysis of genome rearrangement using reversals and block-interchanges.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W696 - W699.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.