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Data Source
The 57,721 rice gene set was provided by TIGR for the NSF rice oligo array project. It is based on The TIGR rice genome project annotation. Note that this set contains over 10,000 transposon sequences that form a big family of their own.
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 57721 |
Maxinum Match Length |
Temperature Seperation
|
15 |
16 |
20°C |
(12636 oligos) |
(25546 oligos, 29180 sec) |
10°C |
(21061 oligos) |
(35831 oligo, 52693 sec) |
|
17 |
15°C |
(35680 oligos ,69947 sec) |
20°C |
(28615 oligos ,156507 sec) |
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