PROBER Tutorial

section 1 - DAS.DNA
section 2 - MerMatch
section 3 - Tolerance
section 4 - PROBER
section 5 - Output


After downloading the *.zip Prober installer file from the 'downloads' section, unzip it into a temporary directory with full directory expansion. If you are using WINZIP then open the zip file, press the extract button and check the 'use folder names' checkbox.

The windows installer will guide you through all the steps for installation. Please note that PROBER must be installed into the C:\PROBER directory.
  If it is not installed into this directory, then you will be unable to run 'MerMatch' or 'Tolerance'.


The following tutorial will guide a user through the necessary steps to create Oligo FISH probes.

Let's begin with a genomic region on chromosome 11 that we have identified as possibly being amplified in Autism.
We will design TOPs (Tiling oligonucleotide probes) for FISH analysis of a 100kb region to determine if a gene (MUC2) in this region is amplified.  MUC2 is located on Chromosome 11 in the UCSC human genome (May,2004 Freeze - HG17).
The coordinates are:

Chromosome 11 : 1,000,000 - 1,100,000 bp

We begin by starting PROBER. Double clicking on the Prober.exe icon (in C:\PROBER or from your desktop) to launch the main application. The software loads a splash screen and then enters the main interface.

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