New Version Released ! (V2.1)

PROBER is an oligonucleotide primer design software application that can generate highly specific probes for use in fluorescence in-situ hybridization (FISH) and other in-situ labeling methods by densely tiling relatively small genomic intervals. Generating Tiling Oligonucleotide Probes (TOPs) requires software capable of masking repetitive genomic sequences and saturating unique contiguous blocks with small (100-2000bp), DNA probes that will generate a single, strong fluorescent signal for regions as small as a single gene.

The program employs a genomic block identification algorithm that we have designed which uses the cumulative sums of areas demarcated as repetitive in order to identify the largest contiguous blocks of unique genomic sequence for the target locus. A probe search algorithm was developed to find the location of the optimal forward and reverse primers of a desired size range within these genomic blocks for probe amplification. In order to test the efficacy of our software, we have designed a number of probes for genomic amplifications that have been detected by Representational Oligonucleotide Microarray Analysis (ROMA) in breast cancer tumor samples. We have determined that PROBER is capable of designing tiling oligo probes for FISH with high genomic specificity both in silico and in vitro.

Prober was written in C# 2005 and has sub-programs that are complied as executables that were written in c, perl and splus. When running PROBER you will need to have the .net framework 2.0 installed on your pc machine.

Nicholas Navin
Wigler Lab
Cold Spring Harbor Laboratory
navin@cshl.edu