Finds Open Reading Frames (ORFs) in each supplied nucleotide sequence, stores found regions as annotations.
Element type: orf-search
Parameters in GUI
| Parameter | Description | Default value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Annotate as (required) | Name of the result annotations. | ORF | result-name | string |
| Search in | Specifies which strands should be searched: direct, complement or both. | both strands | strand | numeric Available values are:
|
| Min length | Ignores ORFs shorter than the specified length. | 100 | min-length | numeric |
| Genetic code | Specifies which genetic code should be used for translating the input nucleotide sequence. | The Standard Genetic Code | genetic-code | string Available values are:
|
| Require init codon | Allows or not ORFs starting with any codon other than terminator. | True | require-init-codon | boolean |
| Require stop codon | Ignores boundary ORFs which last beyound the search region (i.e. have no stop codon within the range). | False | require-stop-codon | boolean |
| Allow alternative codons | Allows ORFs starting with alternative initiation codons, accordingly to the current translation table. | False | allow-alternative-codons | boolean |
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: ORF annotations
Name in Workflow File: out-annotations
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Set of annotations | annotations | annotation-table |