Abstract
BackgroundProcedures for genetic analyses based on oligonucleotide probes are powerful tools that can allow highly parallel investigations of genetic material. Such procedures require the design of large sets of probes using application-specific design constraints.ResultsProbeMaker is a software framework for computer-assisted design and analysis of sets of oligonucleotide probe sequences. The tool assists in the design of probes for sets of target sequences, incorporating sequence motifs for purposes such as amplification, visualization, or identification. An extension system allows the framework to be equipped with application-specific components for evaluation of probe sequences, and provides the possibility to include support for importing sequence data from a variety of file formats.ConclusionProbeMaker is a suitable tool for many different oligonucleotide design and analysis tasks, including the design of probe sets for various types of parallel genetic analyses, experimental validation of design parameters, and in silico testing of probe sequence evaluation algorithms.
Highlights
Procedures for genetic analyses based on oligonucleotide probes are powerful tools that can allow highly parallel investigations of genetic material
This is the case in methods such as the multiplex oligonucleotide ligation assay (OLA) [1], the multiplex ligation-dependent probe amplification assay (MLPA) [2], the RNA- and cDNA-mediated annealing, selection, extension and ligation assays (RASL, DASL) [3,4], the GoldenGate genotyping assay [5], multiplex minisequencing [6], and the padlock or molecular inversion probe assay [7,8]
Tag sequences are added to each probe sequentially in a pattern specified by the user
Summary
Procedures for genetic analyses based on oligonucleotide probes are powerful tools that can allow highly parallel investigations of genetic material. The reaction products generally contain identifying sequences or other features that allow the separation of signals originating from different targets This is the case in methods such as the multiplex oligonucleotide ligation assay (OLA) [1], the multiplex ligation-dependent probe amplification assay (MLPA) [2], the RNA- and cDNA-mediated annealing, selection, extension and ligation assays (RASL, DASL) [3,4], the GoldenGate genotyping assay [5], multiplex minisequencing [6], and the padlock or molecular inversion probe assay [7,8]. This technique uses partially double-stranded oligonucleotides, called selectors, to circularize a selection of restriction fragments from total genomic DNA, and it incorporates a general sequence motif that allows parallel amplification of all circularized fragments using a single primer pair [9]
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