title: PieceMaker: selection of DNA fragments for selector-guided multiplex amplification.
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.
authors.affiliation: Department of Genetics and Pathology, Rudbeck Laboratory Se-751 85, Uppsala, Sweden.
authors.forename: Johan
authors.initials: J
authors.lastname: Stenberg
authors.forename: Fredrik
authors.initials: F
authors.lastname: Dahl
authors.forename: Ulf
authors.initials: U
authors.lastname: Landegren
authors.forename: Mats
authors.initials: M
authors.lastname: Nilsson
mesh_terms: D019295:Computational Biology; D004262:DNA Restriction Enzymes / Q000378:metabolism; D004270:DNA, Circular / Q000737:chemistry; D023281:Genomics; D015345:Oligonucleotide Probes / Q000737:chemistry*; D016133:Polymerase Chain Reaction; D012984:Software
chemical_list: D004270:DNA, Circular; D015345:Oligonucleotide Probes; D004262:DNA Restriction Enzymes