PieceMaker: selection of DNA fragments for selector-guided multiplex amplification
Open Access
- 28 April 2005
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 33 (8) , e72
- https://doi.org/10.1093/nar/gni071
Abstract
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.Keywords
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