1.23.4 Viewing ORFs

  • ORFs appear as an additional annotation layer below the DNA sequence.
  • ORFs in the same frame appear on the same row.
  • Overlapping ORFs in different frames appear on different rows.
  • Non-overlapping ORFs in the same frame or different frames appear in the same row.

  • An ORF sequence highlighted in the sequence view will be simultaneously selected in the adjacent circular/linear view and vice versa (Figure 1.23.4.1).

    Figure 1.23.4.1: ORF Simultenous Viewing.

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Sequence View

  • As in the amino acid layer, the directionality of each ORF is indicated with arrows along the ORF and stop codons are indicated with stars (*).
  • Clicking anywhere in the ORF sequence will automatically select the nearest upstream start codon with its corresponding ORF sequence.

  • Clicking on a Methionine residue within an ORF sequence will automatically select specific sequence range within that ORF (Figure 1.23.4.2).

    Figure 1.23.4.2: ORF Sequence View.

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Linear and Plasmid View

  • ORFs are displayed in the same arrangement as the sequence view, however the directionality of each ORF is indicated with arrow heads.
  • Each Methionine start codon is indicated with a green arrow head, whilst each stop codon is indicated with a red arrow head (according to the directionality of the part).

  • Clicking anywhere in the ORF sequence will automatically select the largest ORF sequence in that region (Figures 1.23.4.3 and 1.23.4.4).

    Figure 1.23.4.3: ORF Linear View.

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    Figure 1.23.4.4: ORF Plasmid View.

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Setting ORF as CDS

  • This can be done from any view and allows you to set an ORF annotation as a CDS feature within the main layer of the sequence.

  • Select the ORF and then "Set as CDS" from the right click drop down menu (Figure 1.23.4.5).

    Figure 1.23.4.5: ORF set as CDS.

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  • The ORF will then be moved to the main layer and annotated as a CDS. Any pre-existing feature annotations will remain but will be split (Figure 1.23.4.6).

    Figure 1.23.4.6: CDS.

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