User GuidesSnapGene Server FeaturesCreate a Feature File for Automatic Feature Detection on SnapGene Server

Create a Feature File for Automatic Feature Detection on SnapGene Server

How do I create a custom feature file for automatic annotation of sequences on SnapGene Server?

This article is provided for SnapGene Server administrators

SnapGene Server uses the same "feature" file type used for SnapGene custom common features. 

Multiple SnapGene custom feature files can be combined into a single feature file that can then be used by SnapGene Server.

Use Case Example: Multiple users within an organization have created their own custom feature sets in SnapGene. This article describes how to locate and combine each users SnapGene custom common feature file into a single custom common features file for use by SnapGene Server.

Create a Copy of one or more SnapGene Custom Features Files

On each computer with a suitably curated custom common feature set (generated within SnapGene, see Edit Common Features), locate and make a copy of the custom common features file customCommonFeatures.ftrs.

On Windows

The customCommonFeatures.ftrs file will be located on path:


\Users\your_user_name\AppData\Roaming\SnapGene\customCommonFeatures.ftrs

 

Note that the AppData folder is hidden by default. In Windows Settings, turn on "Show Hidden folders" then locate the customCommonFeature.ftrs file in Windows Explorer and create a copy.

Alternately, run the "Command Prompt" program and copy the file. Copy and Paste the following command into the Command Prompt window to create a copy on the Desktop called myCCF.ftrs.

copy %HOMEDRIVE%%HOMEPATH%\AppData\Roaming\SnapGene\customCommonFeatures.ftrs %HOMEDRIVE%%HOMEPATH%\Desktop\myCCF.ftrs

On macOS

The customCommonFeatures.ftrs file will be located in the users local Library folder under:

 

\Users\your_user_name\Library\Application Support\SnapGene\customCommonFeatures.ftrs

 

Note the local Library folder is hidden by default.

In Finder, hold down the option key then click menu Go, and choose Library, Application Support, then SnapGene.

Alternately, click menu Go Go to Folder and specify the path as shown below:

~/Library/Application Support/SnapGene

Select and copy the customCommonFeatures.ftrs file (command-c) and paste a copy (command-v) onto your Desktop. 

Rename the .ftrs file to something unique.

On Linux

The customCommonFeatures.ftrs file will be located in a hidden folder .snapgene on path:

 

\Users\your_user_name\.snapGene\customCommonFeatures.ftrs

 

Run the Terminal program to copy the file. Copy and Paste the following command into the Terminal window to create a copy of the .ftrs  file on the Desktop called myCCF.ftrs.

cp ~/.snapgene/customCommonFeatures.ftrs ~/Desktop/myCCF.ftrs

Rename the .ftrs file to something unique.

Copy all .ftrs files to one Computer

A .ftrs file comprises multiple feature regions concatenated into a single sequence. A .ftrs file can be opened and edited in SnapGene.

Copy all .ftrs files to a computer with SnapGene installed.

Prepare .ftrs File Sequences for Concatenation

All .ftrs sequences are concatenated together to give a single sequence using the SnapGene ligation operation. The following step phosphorylates an end of each .ftrs  sequence to allow concatenation.

Finder

Drag and drop each .ftrs file in turn into the SnapGene window.

Click Edit → Edit DNA Ends.

Choose 5' Phosphorylated for the "Right" end, the click OK. Click File → Save to save the changes.

Repeat the phosphorylation step for each .ftrs file.

Concatenate the .ftrs Files by Ligation

Click Actions → Linear Ligation → Ligate (N) Fragments, where (N) is the number of .ftrs to be combined.

Set a .ftrs file as the "Source" for each fragment.

In the "Create Product" field add a suitable name for the "combined" custom features file.

Click Ligate to join the .ftrs files and create a new "combined" custom features file.

Save and Use the New Combined Custom Features File

Click File → Save to save the new "combined" custom features file to an appropriate location.

Copy the "combined" custom features file to your SnapGene Server computer.

Consult the SnapGene Server manual for instructions on defining the path to the new"combined" custom features file.