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Picky allows the parameters to be specified for oligo size, match length, sensitivity, GC content and melting temperature difference. The following is a description of each set of parameters:
Picky will select oligos based on the constraints specified in terms of length, specificity, sensitivity and temperature performance.
| Parameter |
Description |
Oligo Size
Maximum Default: 70
Minimum Default: 50
Ranges: 50 to 90 |
Picky will provide probes with the base size that lies between the minimum and maximum values. |
Match Length
Default: 15
Range: 10 to 25 |
Picky will underline any match that is identical to another sequence by this parameter's given number. These underline sequences will not be contained in any "colored" text probe. |
Sensitivity Level
Default: 10
Minimum: 5 |
Picky will color code base sequences that have high similarities with other continuous sequences. Picky is designed to show pair wise alignment that may give a staggered line of similar results. A lower parameter means a significantly longer computational period. |
GC Content
Default Max: 70
Default Min: 30
Must have a 20-point difference. |
Picky will only select probes within the selected parameter of G and C base percentages. |
Number of Probe Candidates
Default: 100
Range: 50-500 |
Picky will compare the given number based on match region to all non-target genes for the selection of probes. |
Number of Probes per Gene
Default: 1
Range: 1 to 5 |
The number of distinct, non-overlapping oligo probes to be chosen for each sequence. |
Minimum Temp
Difference Default: 20.0
Range: 5.0 to 30.0 |
The difference between a probe candidate's target melting temperature and its highest non-target melting temperature that is considered to be safe. |
DNA Concentration (nanoM)
Default: 1.0 nM
Range: 0.001to 1000.0 nM |
Picky uses this value to calculate melting temperatures between target and non-target genes and need be given as an approximate value. |
Salt Concentration (milliM)
Default: 75 mM
Range: 0.1 to 3000 mM |
Picky will implement this value to calculate hybridization based on melting temperatures. |
These parameters may have a major effect on the computational time and are also limited to a computer's physical memory. Picky needs roughly 20 times the input data size in order to carry out its computation, e.g., for the Maize input set which is about 2.2M bp, Picky will need about 45M total memory to process this set. Also, when the minimum match length is decreased or when the maximum match length is increased, Picky may require an extended time to run when compared to using the default settings.
Click OK on the parameter dialog box.
 
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