Skip Navigation


Bioinformatics Advance Access first published online on March 20, 2008
This version published online on March 24, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn102
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrowOA All Versions of this Article:
24/10/1229    most recent
btn102v2
btn102v1
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
Google Scholar
Right arrow Articles by Nagarajan, N.
Right arrow Articles by Pop, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Nagarajan, N.
Right arrow Articles by Pop, M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published by Oxford University Press 2008.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Scaffolding and validation of bacterial genome assemblies using optical restriction maps

Niranjan Nagarajan 1, Timothy D. Read 2 and Mihai Pop 1,*

1University of Maryland, College Park, MD 20742, USA
2Biological Defense Research Directorate, Naval Medical Research Center and Henry M. Jackson Foundation, 12300 Washington Ave, Rockville, MD 20852, USA

*To whom correspondence should be addressed. Dr. Mihai Pop, E-mail: mpop{at}umiacs.umd.edu


  Abstract

Motivation: New, high-throughput sequencing technologies have made it feasible to cheaply generate vast amounts of sequence information from a genome of interest. The computational reconstruction of the complete sequence of a genome is complicated by specific features of these new sequencing technologies, such as the short length of the sequencing reads and absence of mate-pair information. In this paper we propose methods to overcome such limitations by incorportating information from optical restriction maps.

Results: We demonstrate the robustness of our methods to sequencing and assemby errors using extensive experiments on simulated datasets. We then present the results obtained by applying our algorithms to data generated from two bacterial genomes Yersinia aldovae and Yersinia kristensenii. The resulting assemblies contain a single scaffold covering a large fraction of the respective genomes, suggesting that the careful use of optical maps can provide a cost-effective framework for the assembly of genomes.

Availability: The tools described here are available as an opensource package at ftp://ftp.cbcb.umd.edu/pub/software/soma

Contact: mpop{at}umiacs.umd.edu

Associate Editor: Prof. Alfonso Valencia

Received on January 21, 2008; revised on February 19, 2008; accepted on March 6, 2008

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
 Brief BioinformHome page
M. Pop
Genome assembly reborn: recent computational challenges
Brief Bioinform, July 1, 2009; 10(4): 354 - 366.
[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.