ORF Algorithm Element
The element searches for open reading frames (ORFs) in the provided sequence.
Parameters in GUI
| Parameter | Description | Default Value |
|---|---|---|
| Annotate As | Name of the result annotations. | ORF |
| Direction | See the description here. | Any |
| Allow alternative codons | Allows or disallows ORFs starting with alternative initiation codons, according to the current translation table. | False |
| Require init codons | Allows or disallows ORFs starting with any codon other than a terminator. | True |
| Require stop codons | Ignores or takes into account boundary ORFs which extend beyond the search region. | False |
| Min length | Ignores ORFs shorter than the specified length. | 100bp |
| Max length | Maximum length of annotation allowed. | 10000bp |
| Genetic code | Genetic code that should be used to translate the input nucleotide sequence. | The standard genetic code |
Parameters in Schema File
Type: orf
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| key | Annotate As | string |
| strand | Direction | string |
| Available values are: | ||
| * complement | ||
| * direct | ||
| * both | ||
| alt-start | Allow alternative codons | boolean |
| starts-with-init | Require init codons | boolean |
| ends-with-stop | Require stop codons | boolean |
| min-length | Min length | numeric |
| max-length | Max length | numeric |
| trans-id | Genetic code | string |
| Available values are: | ||
| * “NCBI-GenBank #1” | ||
| * “NCBI-GenBank #2” | ||
| * etc. |