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Data Source
We downloaded NCBI Arbidopsis thaliana UniGene set build version #41 directly from ftp://ftp.ncbi.nih.gov/repository/UniGene/. Since this is a clustered gene set it is much easier to find usable oligos than other genome predicted gene sets.
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 25447 |
Maxinum Match Length |
| Temperature Seperation
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15 |
16 |
20°C |
(17708 oligos) |
(23516s oligos, 15948 sec) |
10°C |
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