PieceMaker: selection of DNA fragments for selector-guided multiplex amplification.
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.
Stenberg
Johan
J
Department of Genetics and Pathology, Rudbeck Laboratory Se-751 85, Uppsala, Sweden.
Dahl
Fredrik
F
Landegren
Ulf
U
Nilsson
Mats
M
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
D004270:DNA, Circular; D015345:Oligonucleotide Probes; D004262:DNA Restriction Enzymes