The Features screen is the first wizard screen of the Map Features template and prompts you to choose the source of the features. The features may be from the source sequence (specified in the Sequences screen) or from a feature file (e.g., a VCF file). You can also specify which features you want to include or exclude when mapping to the target sequence.

This dialog is optional, and you may click Next to instead specify a source sequence on the next screen.

In the Source features section:

  • If your source features are part of an annotated sequence, select From annotated sequence on next page. If they are in a feature or variant (VCF) file, select From feature or variant file and use the Browse button to navigate to the desired file.
  • Use the upper drop-down menu to elect to map All features, Features matching those you will specify in the subsequent row(s) of the dialog, or Features except those specified in the subsequent row(s).

In the Map these features section:

Use the lower drop-down menu to select the feature type to match (or not match), e.g., gene, CDS, exon, intron, mRNA, tRNA, promoter, misc_binding, etc. To specify more than one feature type, use the plus (+) button to add additional “Features” rows. If you want to further limit the search to features matching (or not matching) particular qualifiers, check the Filter box, then choose a qualifier (gene, /product, /locus_tag, /note or /db_xref) from the drop-down menu to its right. In the right-most textbox, enter the text that the qualifier must match or not match (e.g., /gene = thrL) in order for the feature to be removed in the output file. You may use wildcards in this box if you wish (e.g., /gene = thr*).

The image below shows an example of how this section might appear after specifying the desired options:

Click Next to move to the Sequences screen.

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