Finding ORFs

Task Name: find-orfs

This task involves searching for Open Reading Frames (ORFs) in nucleotide sequences and saving the identified regions as annotations.

Parameters:

  • in — A semicolon-separated list of input files. [String, Required]

  • out — An output file containing the annotations. [String, Required]

  • name — The 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 extend beyond the search region (i.e., have no stop codon within the range). [Boolean, Optional, Default: false]

  • require-init-codon — Allows ORFs to start with any codon other than a terminator. [Boolean, Optional, Default: true]

  • allow-alternative-codons — Allows ORFs to start with alternative initiation codons according to the current translation table. [Boolean, Optional, Default: false]

Example:

ugene find-orfs --in=human_T1.fa --out=result.gb --require-init-codon=false
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