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ProbeTools is a probe set design package. This is a software package for designing oligonucleotide probes for OFRG hybridization experiments. The general goal is to design a small collection of probes that will collectively discriminate all, or almost all, clones within a specified population.

The input to the program is a collection of rRNA gene sequences, called the training set, selected by a user. These sequences are assumed to be representative of the targeted population of clones. The program first extracts a number of candidate probes that meet certain criteria specified by the user (length, GC content, etc.) These candidate probes are further processed by a module that removes probes that are not likely to bind in a predictable manner. Then, from among the remaining candidate probes, the program selects the final small collection of probes (typically, between 30 and 50) that optimizes the resolution. More specifically, the goal of selecting the probe set is modeled as a combinatorial optimization problem where we want to compute a set P of k probes, for a given k, that distinguishes the maximum number of clones in the training set. (We say that two clones are distinguished by P, if there is a probe in P that hybridizes with one clone but not the other.) This program was implemented following a heuristic based on the simulated annealing algorithm. (J. Borneman, M. Chrobak, G.Della Vedova, A. Figueroa, and T. Jiang. 2001. Probe selection algorithms with applications in the analysis of microbial communities. Bioinformatics 17(Suppl. 1):S39-S48).

New users, please read instructions.

Please select a training file from the list: Or upload your own training file ( only in FASTA format ):

Required Parameters:
Probe length (<= 15) Number of probes (<= 60) GC content between
% and   %

Advanced Parameters: (you may use the default if you are not sure)
Candidate probe filter Number of probe sets
Iterations before decreasing temperature Steepness of temperature decreasing

You may also add some probes as required probes or delete some probes as forbidden probes:
Required probes: Forbidden probes:


Wait for a few minutes to see the resultant probe set on screen (with low accuracy).

Obtain resultant probe set via email (with higher accuracy), email address:

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Copyright @ by Oligonucleotide Fingerprinting of Ribosomal RNA Genes(OFRG) Group (zliu@cs.ucr.edu, qfu@cs.ucr.edu), 2002

Last Modified on 04/25/2013