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Nucleic Acids Research 2005 33(Web Server Issue):W560-W566; doi:10.1093/nar/gki356
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© The Author 2005. Published by Oxford University Press. All rights reserved
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{at}oupjournals.org

Article

Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies

Sacha A. F. T. van Hijum*, Aldert L. Zomer, Oscar P. Kuipers and Jan Kok

Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen PO Box 14, 9750 AA Haren, The Netherlands

*To whom correspondence should be addressed. Tel: +31 50 3632092; Fax: +31 50 3632348; Email: S.A.F.T.van.Hijum{at}rug.nl

Received December 14, 2004. Revised January 27, 2005. Accepted January 27, 2005.

With genome sequencing efforts increasing exponentially, valuable information accumulates on genomic content of the various organisms sequenced. Projector 2 uses (un)finished genomic sequences of an organism as a template to infer linkage information for a genome sequence assembly of a related organism being sequenced. The remaining gaps between contigs for which no linkage information is present can subsequently be closed with direct PCR strategies. Compared with other implementations, Projector 2 has several distinctive features: a user-friendly web interface, automatic removal of repetitive elements (repeat-masking) and automated primer design for gap-closure purposes. Moreover, when using multiple fragments of a template genome, primers for multiplex PCR strategies can also be designed. Primer design takes into account that, in many cases, contig ends contain unreliable DNA sequences and repetitive sequences. Closing the remaining gaps in prokaryotic genome sequence assemblies is thereby made very efficient and virtually effortless. We demonstrate that the use of single or multiple fragments of a template genome (i.e. unfinished genome sequences) in combination with repeat-masking results in mapping success rates close to 100%. The web interface is freely accessible at http://molgen.biol.rug.nl/websoftware/projector2.


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