|
Data Source
Plasmodium Data Sources: The Plasmodium sequences can also be downloaded from TIGRs Gene Indices site: http://www.tigr.org/tdb/tgi.
The actual FTP URL is as follows: ftp://ftp.tigr.org/pub/data/tgi/Plasmodium_falciparum. Long sequences were broken into pieces to produce the chopped sequences for execution.
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. Beside the maximum_match_len and the minimum_temp_separation parameters; some of other parameters are different only for Plasmodium falciparum, it is listed at the buttom of page; rest of the values are shown:
| maximum_oligo_size = 70 |
minimum_oligo_size = 50 |
| maximum_match_length = ?(see below) |
minimum_match_length = 10 |
| maximum_gc_content = ? (see below) |
minimum_gc_content = ? (see below) |
| candidates_per_gene = 5 |
probes_per_gene = 1 |
| minimum_similarity = 75 |
minimum_temp_separation = ?(see below) |
| 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 9616 |
Maxinum Match Length |
Temperature Seperation
|
15 |
16 |
17 |
20°C |
(4051 oligos, 570 sec)
Max_gc_content=70
Min_gc_content=30
|
(5205 oligos)
Max_gc_content=70
Min_gc_content=30
|
|
10°C |
|
(6117 oligos, 4349 sec)
Max_gc_content=50
Min_gc_content=10
|
(7189 oligos, 14035 sec)
Max_gc_content=70
Min_gc_content=10
|
|
