Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2005 Sep 19:6:229.
doi: 10.1186/1471-2105-6-229.

ProbeMaker: an extensible framework for design of sets of oligonucleotide probes

Johan Stenberg  1 , Mats Nilsson, Ulf Landegren
Affiliations

ProbeMaker: an extensible framework for design of sets of oligonucleotide probes

Johan Stenberg et al. BMC Bioinformatics. .

Abstract

Background: Procedures 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.

Results: ProbeMaker 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.

Conclusion: ProbeMaker 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.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Schematic description of the probe set design procedure. A) Target-specific sequences are first designed for all targets. Tags are then added to each TSS pair in sequence to form complete probes. B) Prior to tag allocation, each TSS pair is evaluated using selected constraints and the current acceptor scheme. Accepted TSS pairs are used to create a series of probe candidates using each valid combination of tags in turn. This procedure is stopped if an acceptable candidate is found, or when all candidates have been tested. A probe is then selected from the list of accepted or temporarily accepted candidates, using the current selector scheme.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Grossman PD, Bloch W, Brinson E, Chang CC, Eggerding FA, Fung S, Iovannisci DM, Woo S, Winn-Deen ES. High-density multiplex detection of nucleic acid sequences: oligonucleotide ligation assay and sequence-coded separation. Nucleic Acids Res. 1994;22:4527–4534. - PMC - PubMed
    1. Schouten JP, McElgunn CJ, Waaijer R, Zwijnenburg D, Diepvens F, Pals G. Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res. 2002;30:e57. doi: 10.1093/nar/gnf056. - DOI - PMC - PubMed
    1. Yeakley JM, Fan JB, Doucet D, Luo L, Wickham E, Ye Z, Chee MS, Fu XD. Profiling alternative splicing on fiber-optic arrays. Nat Biotechnol. 2002;20:353–358. doi: 10.1038/nbt0402-353. - DOI - PubMed
    1. Fan JB, Yeakley JM, Bibikova M, Chudin E, Wickham E, Chen J, Doucet D, Rigault P, Zhang B, Shen R, McBride C, Li HR, Fu XD, Oliphant A, Barker DL, Chee MS. A versatile assay for high-throughput gene expression profiling on universal array matrices. Genome Res. 2004;14:878–885. doi: 10.1101/gr.2167504. - DOI - PMC - PubMed
    1. Oliphant A, Barker DL, Stuelpnagel JR, Chee MS. BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping. Biotechniques. 2002;Suppl:56–8, 60-1. - PubMed

Publication types

MeSH terms

Substances

LinkOut - more resources