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Data Source
We downloaded human mRNAs sequences from NCBI human repository ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/RNA for this sample run. Each sequence has its accession format either in NM_xxxxxx (curated) or XM_xxxxxx (predicted). Certain extra long sequences were broken into 16,384 bp 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. 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 26088 |
Maxinum Match Length |
| Temperature Seperation
|
15 |
16 |
20°C |
(8632 oligos, 3826 sec) |
(16546 oligos, 57032 sec) |
10°C |
(14201 oligos, 3823sec) |
(20050 oligos, 57601 sec) |
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