Skip Navigation



Bioinformatics Advance Access published online on February 17, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl057
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow Supplementary Data
Right arrow All Versions of this Article:
22/9/1064    most recent
btl057v1
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 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 arrowRequest Permissions
Google Scholar
Right arrow Articles by Maydt, J.
Right arrow Articles by Lengauer, T.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Maydt, J.
Right arrow Articles by Lengauer, T.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received December 8, 2005
Revised February 13, 2006
Accepted February 13, 2006

Article

Recco: recombination analysis using cost optimization

Jochen Maydt 1 * and Thomas Lengauer 1

1 Max-Planck Institut für Informatik, Saarbrücken, Germany

* To whom correspondence should be addressed.
Jochen Maydt, E-mail: jmaydt{at}mpi-inf.mpg.de


  Abstract

Motivation: Recombination plays an important role in the evolution of many pathogens, such as HIV or malaria. Despite substantial prior work, there is still a pressing need for efficient and effective methods of detecting recombination and analyzing recombinant sequences.

Results: We introduce Recco, a novel fast method that, given a multiple sequence alignment scores the cost of obtaining one of the sequences from the others by mutation and recombination. The algorithm comes with an illustrative visualization tool for locating recombination breakpoints. We analyze the sequence alignment with respect to all choices of the parameter {alpha} weighting recombination cost against mutation cost. The analysis of the resulting cost curve yields additional information as to which sequence might be recombinant. On random genealogies Recco is comparable in its power of detecting recombination to the algorithm Geneconv (Sawyer 1989). For specific relevant recombination scenarios Recco significantly outperforms Geneconv.

Availability: Recco is available at http://bioinf.mpi-inf.mpg.de/recco/.

Associate Editor: Martin Bishop
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
 Nucleic Acids ResHome page
A.-K. Schultz, M. Zhang, I. Bulla, T. Leitner, B. Korber, B. Morgenstern, and M. Stanke
jpHMM: Improving the reliability of recombination prediction in HIV-1
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W647 - W651.
[Abstract] [Full Text] [PDF]

Home page
 J. Gen. Virol.Home page
J. Fan
Open reading frame structure analysis as a novel genotyping tool for hepatitis E virus and the subsequent discovery of an inter-genotype recombinant
J. Gen. Virol., June 1, 2009; 90(6): 1353 - 1358.
[Abstract] [Full Text] [PDF]

Home page
 JEMHome page
B. F. Keele, H. Li, G. H. Learn, P. Hraber, E. E. Giorgi, T. Grayson, C. Sun, Y. Chen, W. W. Yeh, N. L. Letvin, et al.
Low-dose rectal inoculation of rhesus macaques by SIVsmE660 or SIVmac251 recapitulates human mucosal infection by HIV-1
J. Exp. Med., May 11, 2009; 206(5): 1117 - 1134.
[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.