PROBER Tutorial


Section 4

PROBER: the main interface for probe design

Close the Tolerance & MerMatch window and return to the main PROBER graphical interace



First load in the original (*.fa or *.dna) DNA sequence (from DAS.DNA) by clicking File > Load DNA Sequence

The loaded DNA sequence will appear at the bottom of the program.

Now load the masked (*.mnx1 or *.mnx2) DNA sequence (from MerMatch & Tolerance) by clicking File > Load MNX Sequence.

The loaded MNX sequence will appear at the bottom of the program.




A number of parameters appear in the main PROBER window.

Tier 1 Probe Length : This is the size range in Bp of the final DNA probes, Tier 1 should have a small range.
Tier 2 Probe Length : The size range of the Tier 2 probes should be more relaxed then Tier 1 and have a larger range
Min Tm : This is the minimum primer melting temperature in celsius that is allowed during probe selection (def = 60 C)
Max Tm : This is the maximum primer melting temperature in celsius that is allowed during probe selection (def = 75 C)
Max Repeats : The number of consecutive polynucleotides allowed in the primers
Spacer: This is the number of nucleotides that will be inserted between probes, generally this is set to 0

Set the following parameters for probe selection:

Tier 1 Probe Length : 900 - 1100
Tier 2 Probe Length : 1000 - 1400
Min Tm : 60 C
Max Tm : 70 C
Repeat Nucleotides : 4
MerMatch Length: 18

 

Once the parameters for probe selection are set, click the button in the lower right hand corner - 'Find Probes'

Prober will run for approximately 1 minute, Please proceed to the next section