Exporting Consensus Sequences

To export the consensus sequence for one or more contigs:

1)  Highlight the name of one or more contigs or contig scaffolds in the Project Summary window, or make the Alignment View or the Strategy View the active window.

2)  Select Contig > Save Consensus.

3)  Choose from the following options. Depending on the selected contig(s)/scaffold(s), only a subset of these options may be enabled.

•      Single File – all selected contigs are saved in a single file with the name of your choice. Each contig in the file begins with a note listing the contig name, scaffold ID and scaffold position.

•      Multiple Files – each selected contig is saved as a separate file that is automatically assigned the same name as the contig.

•      As Single Sequence – all selected contigs are joined end-to-end in the same order in which they appear in the Project Summary and saved as a single sequence in one file.

•      One Sequence Per Scaffold –contigs for a given scaffold become a single sequence by being joined end-to-end in the same order in which they appear in the Project Summary. A note listing the scaffold name separates each of the newly-created sequences.

4)  Choose the format for the file(s); different format choices are available, depending on your choice in the prior step.

5)  Choose a location for the file(s), and for single files, type a file name.

6)  Choose the feature and gap options you want:

Check Layout Features if you want to include layout features in the file so that you may view them in another application.

Check Include Gaps only if you want the gaps in the contig(s) to be retained. This is not normally recommended, as a gap signifies no base in that location. If the box is not checked, SeqMan Pro will remove consensus gaps when the contig(s) are saved.

7)  To save, click either Save or OK, depending on your selection in step 3.