Simulates PCR for input sequences and primer pairs. Creates the table with the PCR statistics.
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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 |
Parameters in Workflow File
Type: in-silico-pcr
Parameterprimers-url Primers URL string report-url Report URL string mismatches Mismatches numeric perfect-match Min perfect match numeric
Parameter in the GUI Type
productMax
size
| max- |
| product |
| numeric |
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 |