|
Data Source
The Plasmodium falciparum sequences can also be downloaded from TIGRs Gene Indices site. Here is the actual FTP URL (we choose the release 8 as our data set). Long sequences were broken into pieces to produce the chopped sequences for execution.
Common Design Parameters
Most design parameters of Picky depend on the experimental conditions. The following design parameters are used to generate the collection of oligos in this page. For Plasmodium except for the maximum_match_len, the minimum_temp_separation and minimum_gc_content 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* |
* Note that all Picky reference oligo sets were previously created using Picky 2.0. It is recommended that the new Picky 2.1 be used to redesign any production oligo sets using the hybridization salt concentration from your microarray protocol in order to capture the true benefit of the more precise salt concentration dependant oligo calculation in Picky 2.1.
Variable Design Parameters
Oligo sets can be designed with different stringency 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 decreased. 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
These oligo sets were computed either on a 2-CPU Opteron 246 2.0Ghz workstation with 4G of total memory, or on a 4-CPU Opteron 848 2.2Ghz server with 32G of memory. Both systems are running Redhat Linux Enterprises OS.
Total Sequences: 9518 |
Maximum Match Length |
Temperature Separation |
15 |
16 |
17 |
20°C |
(4199 oligos, 2-CPU, 4m) |
(5424 oligos, 2-CPU, 19m) |
(5924 oligos, 2-CPU, 43m) |
10°C |
(4462 oligos, 2-CPU, 4m) |
(5722 oligos, 2-CPU, 19m) |
(6250 oligos, 2-CPU, 43m) |
(7481 oligos, 4-CPU, 55m)
min_gc_content = 10 |
|
