Find open reading frames

The CLC Genomics Workbench Find Open Reading Frames function can be used to find all open reading frames (ORF) in a sequence, or, by choosing particular start codons to use, it can be used as a rudimentary gene finder. ORFs identified will be shown as annotations on the sequence. You have the option of choosing a translation table, the start codons to use, minimum ORF length as well as a few other parameters. These choices are explained in this section.

To find open reading frames:

        Toolbox | Classical Sequence Analysis (Image gene_and_protein_analysis) | Nucleotide Analysis (Image nucleotideanalyses)| Find Open Reading Frames (Image orf)

This opens the dialog displayed in figure 15.8:

Image readingframedialog
Figure 15.8: Create Reading Frame dialog.

If a sequence was selected before choosing the Toolbox action, the sequence is now listed in the Selected Elements window of the dialog. Use the arrows to add or remove sequences or sequence lists from the selected elements.

The Find Open Reading Frames tool simply looks for start and stop codons and reports any open reading frames that satisfy the parameters. If you want to adjust the parameters for finding open reading frames click Next.