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Nucleic Acids Research 2005 33(8):e72; doi:10.1093/nar/gni071
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Published online 28 April 2005

© 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

Methods Online

PieceMaker: selection of DNA fragments for selector-guided multiplex amplification

Johan Stenberg, Fredrik Dahl, Ulf Landegren and Mats Nilsson*

Department of Genetics and Pathology, Rudbeck Laboratory Se-751 85, Uppsala, Sweden

*To whom correspondence should be addressed. Tel: +46 018 471 4816; Email: Mats.Nilsson{at}genpat.uu.se

Received February 11, 2005. Revised April 1, 2005. Accepted April 1, 2005.

We describe PieceMaker, a software tool for the design of applications of selector probes–oligonucleotide probes that direct circularization of target nucleic acid molecules. Such probes can be combined in parallel to circularize a selection of fragments from restriction digested total genomic DNA. These fragments can then be amplified in a single PCR using a common primer pair, yielding substrates for subsequent analyses, such as parallel genotyping or sequencing. However, designing multiplex selector assays is a laborious task. The PieceMaker program alleviates this problem by selecting restriction enzymes to generate suitable fragments for selection, and generating the output data required to design the selector probes.


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