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Data Source
The maize sequences used in this sample run were extracted from the ISU maize genomic assembly MAGI3.1 (http://www.plantgenomics.iastate.edu/maize/)based on FGENESH (Softberry, Inc., NY) predictions using default Monocot settings. Exonic regions predicted by FGENESH for individual MAGIs were extracted and assembled into new corresponding sequences that mimic the predicted transcript sequences and used as Picky's input. Resulting sequences of length less than 50 bp were excluded and not analyzed by Picky.
Common Design Parameters
Most design parameters of Picky depends on the experimental conditions. The following design parameters are used to generate the collection of oligos in this page. Except for the maximum_match_len and the minimum_temp_separation parameters, all the other parameters are fixed and their values are shown:
| maximum_oligo_size = 70 |
minimum_oligo_size = 50 |
| maximum_match_length = 15 |
minimum_match_length = 10 |
| maximum_gc_content = 70 |
minimum_gc_content = 30 |
| candidates_per_gene = 5 |
probes_per_gene = 1 |
| minimum_similarity = 75 |
minimum_temp_separation = 20 |
| DNA_concentration = 1 |
Salt_concentration = 75 |
Variable Design Parameters
Oligo sets can be designed with different strigency by varying the maximum match length and minimum temperature separation parameters of Picky. Generally, a bigger oligo set can be produced when the maximum match is increased, or when the minimum temperature is descreased. However, making those changes also decreased the discriminative power of the oligo designed. Therefore, it is up to the users to decide which oligo set gives them the best balance between number of oligos and the discriminative power. A picture is provided below to illustrate the difference:
Download Oligo Sets
Total Sequences 44729 |
Maxinum Match Length |
| Temperature Seperation
|
15 |
16 |
20°C |
(18816 oligos, 2006 sec) |
(24457 oligos, 7768 sec) |
10°C |
|
(35022 oligos, 10526 sec) |
|
