ArticleBMC bioinformatics2005
ProbeMaker: an extensible framework for design of sets of oligonucleotide probes.
Article in BMC bioinformatics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Article
- Simultaneous In Situ Detection of mMethods in molecular biology (Clifton, N.J.) · 2024Article
- Oligonucleotide Fluorescence In Situ Hybridization: An Efficient Chromosome Painting Method in Plants.Plants (Basel, Switzerland) · 2023Review
- Guidelines for the Optimization and Validation of In Situ Hybridization.Methods in molecular biology (Clifton, N.J.) · 2020Article
- OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- New lung cancer panel for high-throughput targeted resequencing.Genomics & informatics · 2014Article
- Article
- Colorimetric nucleic acid testing assay for RNA virus detection based on circle-to-circle amplification of padlock probes.Journal of clinical microbiology · 2011Article
- Targeted resequencing of candidate genes using selector probes.Nucleic acids research · 2011Article
- Multiplexed genotyping of methicillin-resistant Staphylococcus aureus isolates by use of padlock probes and tag microarrays.Journal of clinical microbiology · 2009Article
- Disperse--a software system for design of selector probes for exon resequencing applications.Bioinformatics (Oxford, England) · 2009Article
- A single molecule array for digital targeted molecular analyses.Nucleic acids research · 2009Article
- Simultaneous genotyping of all hemagglutinin and neuraminidase subtypes of avian influenza viruses by use of padlock probes.Journal of clinical microbiology · 2008Article
- Multigene amplification and massively parallel sequencing for cancer mutation discovery.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- In vitro analysis of DNA-protein interactions by proximity ligation.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- MLGA--a rapid and cost-efficient assay for gene copy-number analysis.Nucleic acids research · 2007Article
- PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens.BMC bioinformatics · 2006Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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