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