Enumerate candidate ORFs
computase_enumerate_orfsFind all open reading frames (ORFs) in a nucleotide sequence by scanning all six reading frames, with adjustable start/stop codon requirements and genetic code tables.
Instructions
Enumerate bounded candidate ORFs across all six reading frames.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| sequence | Yes | Raw nucleotide sequence or one FASTA record; IUPAC codes are accepted. The normalized sequence is limited to 5,000,000 nucleotides. | |
| table_id | No | NCBI genetic-code table identifier. | |
| max_results | No | Maximum returned candidates. | |
| require_stop | No | Require an in-frame terminal stop codon. | |
| start_codons | No | Allowed start-codon policy. | table-starts |
| min_length_nt | No | Minimum nucleotide span including stop. | |
| include_nested | No | Report starts nested before the same stop. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| note | No | Scientific interpretation boundary. | These are candidate ORFs, not gene predictions. |
| orfs | Yes | Candidate ORFs in deterministic coordinate order. | |
| truncated | Yes | Whether candidates were omitted by max_results. | |
| parameters | No | Effective operation parameters, excluding the input sequence. | |
| total_found | Yes | Total candidates found before result limiting. | |
| computase_version | No | Computase version used for the computation. | 0.1.1 |
| coordinate_system | No | 0-based-half-open |