In Silico PCR Element
Simulates PCR for input sequences and primer pairs. Creates a table with PCR statistics.
Element type: in-silico-pcr
Parameters
| Parameter | Description | Default Value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Primers URL | A URL to the input file with primer pairs. | primers-url | string | |
| Report URL | A URL to the output file with the PCR report. | report-url | string | |
| Mismatches | Number of allowed mismatches. | 3 | mismatches | numeric |
| Min perfect match | Number of bases that match exactly on 3’ end of primers. | 15 | perfect-match | numeric |
| Max product size | Maximum size of amplified region. | 5000 | max-product | numeric |
| Use ambiguous bases | Search for ambiguous bases (as “N”) if checked. | True | use-ambiguous-bases | boolean |
| Extract annotations | Extract annotations within a product region. | Inner | extract-annotations | string |
Input/Output Ports
The element has 1 input port:
Name in GUI: Input sequence
Name in Workflow File: in-sequence
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Sequence | sequence | sequence |
And 1 output port:
Name in GUI: PCR product
Name in Workflow File: out
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Set of annotations | annotations | annotation-table |
| Sequence | sequence | sequence |