Editing in Genome Workbench

Step 1: Prepare Genome Workbench for editing

Launch Genome Workbench.

Go to the Tools menu and pick Packages.

Packages menu

Make sure that the Sequence Editing package is Loaded. (Sequence Editing may appear as "Sequence E …") If not, click on the Sequence Editing package, check the "Enabled" checkbox, click OK, exit Genome Workbench, and re-launch Genome Workbench.

Packages 1

Packages 2

Packages 3

Packages 4

Step 2: Open a FASTA file for editing

Click on the File menu at the top left or the open file folder just below it.

File open 1

Click on "File Import" on the left side of the dialog.

File open 2

Choose "Autodetect Format" for File Format.

Click the button to browse for a FASTA file and choose your file.

Click Next. Leave options as defaults (Sequence Type should be Autodetect, leave all checkboxes unchecked except "Parse all Sequence IDs" and "Skip sequences with invalid defines".

File open 3

Click Next.

Choose "Create a new Project".

File open 4

Click Finish.

File open 5

Step 3: Open a Text View to see the sequences in the GenBank FlatFile representation

Right-click on the item under “Data” in the New Project you have created on the left side.

Text view 1

Click on "Open New View".

Scroll down to Generic.

Text view 2

Click on Text View.

New Text View should open.

Click onOptions button at upper right hand of new view.

Text view 3

Change Format to "Flat File".

Text view 4

Click on OK.

Text view 5

Right click in newly created Text View and click onExpand All.

Text view 6

Text view 7

Step 4: Create a gene feature with locus “ABC” on the first 25 NT of the first sequence

On the right-hand side of the top bar for the Text View, from the dropdown list next to Sequence(s), pick the sequence ID for your first sequence.

Create feature 1

Click on the Annotate menu. Choose Genes and Named Regions->Gene.

Create feature 2

The Edit Object dialog should appear. Enter "ABC" in the box next to Locus.

Create feature 3

Click on "Location" on the left.

Create feature 4

In the box under "To" change the number to 25. Leave the number under "From" as 1.

Create feature 5

Click Ok.

The gene you have created should now appear in the FlatFile display.

Create feature 6

Step 5: Add a coding region with product name “hypothetical protein” to every sequence in your record

Click on the Annotate menu, choose Batch Feature Apply->Add CDS.

Bulk apply CDS 1

The Add Features dialog should appear. In the "Protein Name" box, type "hypothetical protein".

Bulk apply CDS 2

Click Ok.

You should now see a coding region with product "hypothetical protein" in the FlatFile display.

Bulk apply CDS 3

Click on the list next to Sequence(s) at the upper right hand side of the Text View. You should now see your nucleotide sequences interspersed with the IDs for newly created protein sequences.

Bulk apply CDS 4

Use the list to navigate to a different nucleotide sequence in your record and see that there is now a coding region there also.

Bulk apply CDS 5

Current Version is 3.6.0 (released March 04, 2021)

Release Notes





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Last updated: 2017-11-04T03:25:26Z