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Open reading frames

The ORFs tab lists open reading frames: stretches that start with ATG and run in frame to the first stop codon, on both strands, including frames that cross the origin of a circular sequence. The list updates in the background whenever the sequence changes.

Starts that share a stop are one ORF, listed from the farthest start — also when that start is on the other side of the origin, so an ATG just after the origin is not listed a second time inside the ORF that comes round to it. On a circle an ORF is at most as long as the sequence: a start whose reading would come all the way round before it stops is skipped for the next start that fits, and a reading with no stop at all is no ORF.

Each row shows the strand (→ forward, ← reverse), the range in 1-based coordinates (including the stop codon) and the length of the protein in amino acids. The list is sorted by position.

While the tab is open, every ORF listed is also drawn on the map and in the sequence view, as a dashed arrow on its own strand labelled with its length (see Previews); clicking one there selects it, as clicking its row does. Past 200 ORFs none are drawn — lower the count with Minimum length.

Minimum length

Only ORFs of at least Minimum length codons (not counting the stop) are listed; the default is 75 codons, about 225 bp. Lower it to see short peptides, raise it to keep the list to real genes. Press Enter or leave the field to apply.

Genetic code

Code chooses the genetic code the scan reads with. It decides where an ORF ends as well as where it may begin: under the standard code the stops are TAA, TAG and TGA, while under the vertebrate mitochondrial code TGA is tryptophan and AGA/AGG are stops instead — so a mitochondrial gene scanned with the standard code is cut short at the first TGA.

It is the same choice as the Translate tab's, one for the app rather than per document, and it is remembered. A CDS feature is not affected: those are always read with their own /transl_table.

Working with an ORF

  1. Click an ORF to select it. Both views scroll to it.
  2. ORF translation below the list shows the protein, with the first codon as M and the stop as *.
  3. Copy protein puts the amino-acid sequence on the clipboard.
  4. Add as CDS feature annotates the ORF as a CDS with /codon_start=1 and the /translation, opens the Features tab and lets you type the name straight away. When the code is not the standard one it writes /transl_table too, so the feature reads back the way it was found. Right after an edit it is greyed out until the ORFs have been found again: an edit outside an ORF can still move where it starts or ends.

If some other range is selected (not an ORF from the list), the tab shows the translation of that selection in frame +1 instead, so you can check any stretch of at least three bases. For all six frames at once, use the Translate tab.