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Bioinformatics Advance Access originally published online on April 26, 2007
Bioinformatics 2007 23(13):1573-1579; doi:10.1093/bioinformatics/btm153
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

OSLay: optimal syntenic layout of unfinished assemblies

Daniel C. Richter 1,*, Stephan C. Schuster 2 and Daniel H. Huson 1

1Center for Bioinformatics (ZBIT), Institute for Computer Science, Tübingen University, 72076 Tübingen, Germany and 2Penn State University, Center for Comparative Genomics and Bioinformatics, University Park, PA 16802, USA

*To whom correspondence should be addressed.


  Abstract

Summary: The whole genome shotgun approach to genome sequencing results in a collection of contigs that must be ordered and oriented to facilitate efficient gap closure. We present a new tool OSLay that uses synteny between matching sequences in a target assembly and a reference assembly to layout the contigs (or scaffolds) in the target assembly. The underlying algorithm is based on maximum weight matching. The tool provides an interactive visualization of the computed layout and the result can be imported into the assembly editing tool Consed to support the design of primer pairs for gap closure.

Motivation: To enhance efficiency in the gap closure phase of a genome project it is crucial to know which contigs are adjacent in the target genome. Related genome sequences can be used to layout contigs in an assembly.

Availability: OSLay is freely available from: http://www-ab.informatik.unituebingen.de/software/oslay

Contact: drichter{at}informatik.uni-tuebingen.de

Associate Editor: Martin Bishop

Received on January 16, 2007; revised on March 27, 2007; accepted on April 16, 2007

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