In order to use Genome Compiler, you can work with any computer running the latest Chrome / Firefox / Safari / Explorer. The minimum preferred screen resolution is 1366 x 768.
Getting Started with Genome Compiler
Genome Compiler supports Windows and Mac operating systems.
Genome Compiler supports the following browsers:
- Google Chrome
- Mozilla Firefox
- Internet Explorer
Using the online version allows you to instantly login to the software from a browser on any computer, anywhere you are. Using the downloadable version is possible after you download and install it on your computer - therefore, you have to download Genome Compiler on each computer you want to use it on.
All of the features and tools are available in both versions, however, with the downloadable version you need an internet connection in order to use some of the features. For example, auto annotation, clustalW alignments, primer3 and in order to save your data on the cloud and share files with your colleagues.
Additionally, on the online version, your files are saved on to the cloud where they are automatically backed-up. On the downloadable version, data can be saved locally - on your computer or on the cloud. If files are only saved locally, they will not be backed-up.
If you’re using both versions, it’s better to save your files on the cloud. The reason is that data that is saved on the cloud is synced between the downloadable and online versions so you can access it anywhere.
In order to use the Genome Compiler’s downloadable version, you’ll need to install Adobe AIR. Simply download it and follow Adobe’s quick installation guide. After Adobe AIR is installed, you can then download Genome Compiler.
If you haven't signed up already, follow the Genome Compiler’s sign up steps. During the sign-up you will be asked to choose between the online version and the downloadable one. Notice that it’s always possible to change your mind - whether you started online or not.
If you proceeded to initially use the online version, and you would now like to download the software, you can request this from the online version “Help” menu. Simply click “Get a desktop version” and we will send you the download link.
In order to verify your account, look for the confirmation email from Genome Compiler on your inbox. Activate than your account by simply pressing ‘Activate’.
In case you can’t find the confirmation email in your inbox, check the spam folder or Gmail’s Social or Promotions folders - where it usually goes to automatically. If you can’t find it there as well, you can always contact us for help: firstname.lastname@example.org.
- In most cases, unsuccessful installation of Genome Compiler software can be solved by these simple actions:
- Temporarily disable your antivirus - the Genome Compiler installer is sometimes blocked by antiviruses.
- Make sure the file is located locally on your computer and not on a shared drive.
- The Genome Compiler installation file should be a .air file. If the installation file is a .zip file instead, make sure you use Firefox or Google Chrome to download Genome Compiler.
- You can always contact us to email@example.com for support.
You will be prompted with a message from Genome Compiler when there are software updates. If by any chance you didn't update when prompted, you can check for updates at any time from the help menu.
Importing My Data
Yes, we support most file formats created by other biology software tools, such as Vector NTI, SnapGene, Geneious, Clone Manager, Serial Cloner, Plasma DNA, ApE, DNAStar, etc.
We are continually expanding the import support of other file formats whereby the DNA sequences in addition to feature annotations are maintained. To see the full list of supported file formats, please visit our user manual page “Importing and Exporting".
The quickest way is to open the File menu and select Import Primers. A dialogue will open up prompting you to choose the file containing your primers from your computer. Make sure your primers are saved as one of the following file formats:
- Vector NTI primer database (.oa4)
- Plasma DNA database (.pdat)
- Comma Separated (NAME,SEQUENCE,OVERHANG)
- Tab Separated (NAME SEQUENCE OVERHANG)
- Semicolon Separated (NAME;SEQUENCE;OVERHANG)
Once you have chosen the file from your computer, the primers will appear a table in the opened dialogue box. Using the check boxes, select which ones you would like to import. Then choose a library for saving your primers into. You can choose an existing library or create a new one.Then click Import and your selected primers will be imported into your chosen library in Genome Compiler. Learn more about Primer Libraries in our user manual.
In order to align a sequence against a template, first open the template sequence and then press “Align” in the toolbar. This will open up a settings dialog where you can either drag and drop sequences from your Materials box to align, paste sequence to align, or choose sequences from your computer to align. It is important to note that chromatograms (from .AB1 or .SCF files), can only be visualised as alignments against a template sequence if they are uploaded this way.
Alternatively, in order just to view the chromatogram without aligning it against a template you can just import .AB1 or .SCF files through the regular file import flows, e.g. File menu → Import file. Learn more about sequence alignment in our user manual.
Yes. You can take quick snapshots by clicking on the small camera icon on the top right of the sequence and the linear and circular views of your opened project.
Embedded Databases & Organizing Projects
All your saved data and projects are stored inside the Materials Box which is easily accessible on the left side of Genome Compiler’s interface. You can create specific folders inside the Materials Box to organise your saved data and projects.
Genome Compiler has an embedded library, found inside the Materials Box, which contains sub folders of Addgene, Sigma Aldrich and Synberc plasmid repositories, as well as the iGEM parts repository, and other useful genomes, parts and plasmids.
In addition, there is an auto annotation library, containing the Plasmapper database of parts, including hundreds of commonly used coding sequences, promoters and terminators and more, which can be “Blasted” against to auto annotate your sequences.
It is also possible to query the NCBI database from within Genome Compiler and then instantly import your data into the Materials Box directly from Genome Compiler.
It is possible to query the NCBI database directly from within Genome Compiler and then instantly import your data into the Materials Box directly from Genome Compiler.
In addition, you can directly import and use sequences and parts from the embedded databases of Sigma-Aldrich, Synberc and AddGene inside the Genome Compiler's Materials Box.
We save a copy for 30 days so your deleted projects and data can be restored. After these 30 days, it will be permanently deleted.
Sharing and Review
Whole primer libraries, whole auto annotation libraries and whole folders containing sequences (of genomes, parts or vectors) can be shared easily over the cloud in Genome Compiler.
Just right click on the root folder and select “Share”. Then type the email address of the colleague with whom you would like to share the folder with, and then assign read/write or read-only permissions.
It is important to note that only whole folders can be shared. It is not possible to share sub-folders or single projects inside folders.
First, create an account and have this as the master account and import all your data. The master account will be the ‘Owner’ of the folders.
Then have every other lab member create their own account. From the master lab account, share the folders containing your imported data with every other lab member. Right click on the folders and instead of “Share,” click “Settings” - this way is more convenient to add multiple collaborators simultaneously to have access to a folder. Type the email addresses of each lab member, assign permissions and then select “Ok.”
Each lab member will now see these folders appear in their Material box in their account.
It is possible to make comments on a stretch of sequence by simply highlighting the sequence and selecting “Add comment”. The comment will then appear on the sequence along with the author and date of the comment, and is indicated with a small yellow flag.
All of these comments are saved in a “Summary Table” per project, which can be opened from the “Annotation Layers” menu at the bottom right of an opened project.
In the far right column of the table it is possible to see the author of each comment and clicking on each comment in the table will take you to the exact area in the sequence where the comment was made.
When the first user saves a project, the next user/s will be prompted to save a new copy. This is similar to how Dropbox works. However, there are no duplication risk because a new copy will anyway be created.
Genome Compiler currently supports the Restriction Ligation and Gibson Assembly cloning methods. You can use the cloning wizards to guide you through your cloning, step by step.
Some users have told us it is possible to adapt the Gibson Cloning Wizard. You just have to use your target as the vector backbone, set it as a PCR amplification using 50 bp primers and use only one insert. Then, you just use the primer output for the insert and ignore the primer results for the vector backbone.
You can use our cloning wizard for Restriction Ligation to help you pick primers. Via this Restriction Ligation wizard, the insert sequence will be scanned for endogenous restriction sites and you will be guided to choose appropriate sites in your vector. Compatible restriction sites will be added onto the ends of your primers and hence added onto the ends of your insert sequence. You will need to add some additional 5’ nucleotides necessary for efficient cutting in the “Leader Sequence” field.
Or you can design primers yourself in the opened project, by either clicking on the “Primer” icon in the toolbar and click on “Auto design (Primer3)” or “Manual primer design” to open up the relevant dialog. Or select the sequence in the project where you would like to create the primer and right click and select “Create primer from selection.” This will open up the “Manual Primer Design” dialog. You can make mismatches and add overhang sequence such as restriction sites, spacer sequences (including peptides, specific amino acids etc), and leader sequences.
Sequence Annotation and Feature Keys
Select the sequence you would like to annotate and then press “Annotate Selection.” This will create a new part and open up a new tab on the right side called “More Properties.” From this tab there are options to set the annotation name, the annotation feature key and the strand, in addition to more.
You first need to annotate the sequence as a coding sequence (CDS); select the sequence you would like to annotate and then right click and select "Annotate Selection."
This will then open up a tab on the right, called "More Properties." In this tab you will see there is a Feature Key section, select the CDS Feature Key, and then immediately you should see the translation appear under the sequence on the left.
If at any point in time you would like to hide this translation, just go to the bottom right of the opened project and open up the "Annotation Layers" menu. Then, uncheck the tick-box for "Amino acids."
- Genome Compiler uses the industry's best security measures ensuring your data can be accessed only by you. The data is stored on Amazon infrastructure to ensure the best in class reliability. Data is transferred to you through a secure HTTPS channel making sure only you can see your data.
- All of your sequences on Genome Compiler are private and proprietary. Others can access these sequences in case you've shared it with them using Genome Compiler sharing features or if you give your credentials to others.
There are several options for you to learn how to use Genome Compiler and get things started - just decide what works out best for you:
- The helper tips - After signing up and starting to use the software, you will be prompted with helpful tips to help you get it started. Also, upon your first use of our features, you’ll receive these tips as well.
- The user manual - this contains a thorough guide of the software - starting from the basics actions to a deep look into the features as well as guides how to convert from other software tools to Genome Compiler.
- The tutorials - these short videos will make you a Genome Compiler expert by learning how to use the specific features on the software. Just pick the topic that you’re interested in and quickly learn how to do it yourself.
- The webinars - we are conducting live webinars from time to time, about new features we've added or even just explaining the basics again for beginners. If you can’t wait for the live ones, you can watch the recordings. We will send you invitations for the next live webinars.
You can contact us for support at any time through our website and/or the software. You can do so by several ways:
- The best way to contact us is via the live chat, where you can talk directly to a Genome Compiler representative. The live chat can be found on the bottom right of the interface inside the software.
- On the “Help” menu inside the software you can leave us a feedback, contact us or report a bug.
- From our website - through the “Contact us” button.
- Email to firstname.lastname@example.org