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ProbeMaker 1.4 released

2006-07-07

A new version of ProbeMaker released at 070606.

Related projects:

- AppTools
- MolTools library

Links:

-The EU FP6 MolTools program

Welcome to ProbeMaker!

  1. What is ProbeMaker?
  2. Feature list
  3. Description and user guide
  4. Extensions
  5. How do I get ProbeMaker?
  6. How do I cite ProbeMaker?
  7. Contact information

What is ProbeMaker?

ProbeMaker is a Java software project aimed at providing a framework for design and analysis of sets of oligonucleotide probes for use in multiplex assays for nucleic acid analyses and other purposes.

The ProbeMaker software is free, open-source software and all users are invited to contribute to the further development of the software, both by writing new extensions and by suggesting/making improvements to the program core.

The principal developer is Johan Stenberg of the Molecular Medicine research group at the Department of Genetics and Pathology, Uppsala University, Uppsala, Sweden

ProbeMaker provides a platform for design and analysis of sets of oligonucleotide probes. Briefly, a set of target sequences is provided to the software and a probe is designed for each target. The design involves, among other things, the analysis of target and probe sequences by a selection of analysis modules.

The choice of target type and analysis modules determines what task the software will perform. This could range from simple Tm calculation of a number of probe-target hybrids, to the evaluation of a set of primers for multiplex PCR, or the design of a set of allele-specific padlock probes for a set of polymorphic targets.

ProbeMaker supports probes made up of separate elements, or subsequences. Each probe consists of up to two elements whose sequences are determined by the target sequence and a number of elements for other purposes, such as amplification, hybridization or identification.

The sequence elements that are determined by the targets, called 'target-specific sequences' or 'TSSs' for short, are generally designed to hybridize somewhere on the target sequence, and to have a certain hybridization temperature or to be of a certain length.

Other sequence elements, called 'tags' in the ProbeMaker software, may be added to the probes in different patterns to yield tags that are common, locus-specific, allele-specific or unique among the probes. These tags are selected from sets of sequences that are provided by the user. Depending on the pattern in which tags are used, several candidates may be possible for each probe.

Probe candidates are generated and evaluated by performing a number of tests on each candidate. These tests are selected by the user, and may include tests for unwanted interactions within probes, between probes and target sequences or between probes.

A plug-in mechanism in the software makes it possible to include target types that define the positioning of target-specific sequences, and to define and add tests. This mechanism, in combination with the possibility to add tags in different positions and patterns, makes it possible to use ProbeMaker for the design of many different types of probes.

Furthermore, new input and output formats may be defined and added that make it possible to use data from various sources and to output the probes in different formats for downstream processing.

Feature list

Description and user guide

See the ProbeMaker description for a detailed description of the software.

See the ProbeMaker tutorial to get started using ProbeMaker.

See the ProbeMaker examples to see some example uses of ProbeMaker.

Extensions

The ProbeMaker software is of limited use without application-specific extensions. These include different types of targets and file formats, as well as analysis modules for testing of different types of probes. New extensions may be written and easily included through the plug-in mechanism. A programmer's guide for writing extensions will be available shortly, until then the ProbeMaker API available from the project site may be used for instructions.

Some extensions are provided with the current release of ProbeMaker, see the list of available extensions for descriptions and the project site for files.

How do I get ProbeMaker?

ProbeMaker is provided 'as is', without express or implied warranties of any kind.

Java 1.4 or later is required to run ProbeMaker.

The ProbeMaker software is distributed under the terms of the GNU General Public License. Downloading the software implies accepting these terms.

ProbeMaker requires the MolTools library, and the AppTools library. These libraries are distributed under the GNU Lesser General Public License and are bundled with the ProbeMaker distribution.

The software is available as a Java archive (jar) file, and as a zip file. The jar file contains all class-files required to run the software. The zip file is a convenience file for Microsoft Windows users, containing various configuration files that otherwise must be created manually.

The files are available from the project site.

How do I cite ProbeMaker?

If you use ProbeMaker in your research, please cite:

Stenberg, J., Nilsson, M., and Landegren, U. ProbeMaker: an extensible framework for design of sets of oligonucleotide probes. BMC Bioinformatics 2005, 6:229

If you use extensions built on algorithms from other developers, please cite the original work as well.

Contact information

For questions and comments, please refer to the project site on SourceForge