Task Name: find-orfs
Searches for Open Reading Frames (ORFs) in nucleotide sequences and saves the regions found as annotations.
Parameters:
in — semicolon-separated list of input files. [String, Required]
out — output file with the annotations. [String, Required]
name — name of the annotated regions. [String, Optional, Default: “ORF”]
min-length — ignores ORFs shorter than the specified length. [String, Optional, Default: 100]
require-stop-codon — ignores boundary ORFs that last beyond the search region (i.e. have no stop codon within the range). [Boolean, Optional, Default: false]
require-init-codon — allows ORFs starting with any codon other than terminator. [Boolean, Optional, Default: true]
allow-alternative-codons — allows ORFs starting with alternative initiation codons, accordingly to the current translation table. [Boolean, Optional, Default: false]
Example:
| Code Block |
|---|
ugene find-orfs --in=human_T1.fa --out=result.gb --require-init-codon=false |