ORF Marker Element
Identifies Open Reading Frames (ORFs) in each supplied nucleotide sequence and stores the identified 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: | ||||
| * 0 - for searching in both strands | ||||
| * 1 - for searching in the direct strand | ||||
| * 2 - for searching in the complement strand | ||||
| 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: | ||||
| * NCBI-GenBank #1 | ||||
| * NCBI-GenBank #2 | ||||
| * etc. | ||||
| Require init codon | Specifies whether ORFs starting with a codon other than the initiator are allowed. | True | require-init-codon | boolean |
| Require stop codon | Ignores boundary ORFs that extend beyond the search region (i.e., have no stop codon within the range). | False | require-stop-codon | boolean |
| Allow alternative codons | Allows ORFs to start with alternative initiation codons according 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 |