Export Sequences Dialog Box Features

The dialog box has the usual file selection controls, and in addition the following options. On Windows, you can choose to show the native file selector separately from the options—see File chooser dialogs (Windows only) options.

• Export controls
  • Sequence selection menu
  • Alignment selection menu
  • Preserve relative indices option
• Save also options
  • Secondary structure annotation codes option
  • Similarity values option
  • Computed descriptors option
  • Annotation values option
• Format options
  • Create a new file for each option

Export controls

The Export: option menus allow you to control which sequences and which parts of the sequences are exported.

Sequence selection menu

Choose which sequences to export, from Displayed Sequences, All Sequences, or Selected Sequences.

Alignment selection menu

Choose which parts of the sequences to export.

• Full Alignment—export the entire range of residues in all the sequences chosen for export.
• Selected Blocks—export only the blocks of the sequences that are selected in all sequences chosen for export.

Preserve relative indices option

If you choose to export selected blocks, select this option to preserve the relative indices of each sequence. This is done by converting everything that wasn't included in the selected blocks to a gap in the output sequence.

If not checked, the selected blocks are renumbered starting with index 1, and a single gap is inserted between the blocks to demarcate them.

Save also options

Select options for the data to be saved with the sequences. These options are not available if the file type is CLUSTAL.

Secondary structure annotation codes option

Save the SSP and SSA annotations in the file. This option is only available for FASTA and SeqD formats.

Similarity values option

Save the calculated percent similarity between sequences, if exporting the full alignment. The values are added to the sequence name as ID (identity), SIM (similarity), HOM (homology), e.g.

 >1abc|ID:7.14|SIM:19.64|HOM:17.86

Computed descriptors option

Export the descriptors computed in the protein sequence descriptors, as extra columns in a CSV or SeqD file.

This option is only available if the file type is CSV or SeqD and the descriptors have been computed. Note: Some descriptors are not computed per residue, but only for the whole sequence. These will not be included in the SeqD file.

Annotation values option

Select this option to include annotations that are calculated on a per-residue basis when exporting to a SeqD file: Residue Number, Predictions (for secondary structure, solvent accessibility, domain arrangement, and disordered regions), Kinase features, GPCR Regions, and Custom Annotations.

Format options

Specify how the sequences are distributed between files.

Create a new file for each option

Export the sequences to separate files rather than a single file either as a set of chains or as individual chains. The file name is constructed from the sequence title; the chain name is added if exporting chains.

• Chain—Export each chain in each sequence to a separate file.
• Structure (all chains)— a set of chains with the same sequence title (not necessarily that there is a 3D structure associated with the chains). This option is useful if you want to export the heavy and light chains of an antibody to the same file.

Note: If the SeqD file format is selected, the Create a new file for each option will be selected by default, and cannot be deselected.