Here is the last feature i have implemented for the upcoming Assemble2 1.2. We will start with an RNA secondary structure displayed in Assemble2 (and predicted from the sequence stored in the sample file ft3100_from_FANTOM3_project.fasta). I have selected the prediction from the algorithm RNAfold.
Now I would like to submit this sequence to the mfold Web server. By choosing Plugins | mfold Web Server, this opens the RNA folding form inside Assemble2. Once the web page loaded, and if a secondary structure is displayed, the name and the sequence are automatically filled in the form.
Once the button “Fold RNA” clicked, the sequence is reformatted by the website, indicating that the prediction has been correctly submitted. I have observed that the website is a little bit less reactive through Assemble2, but nothing dramatical. After a while, you should get the predictions. They’re listed on the web page (the blue arrow in the next screen capture), and Assemble2 lists them also in a choice box (the red arrow in the next screen capture).
Now i can use this choice box to select the prediction/structure #5 (for example) to see and manipulate it in Assemble2. To do so, i click on the button on the right (the red arrow in the next screen capture). And it’s done!!
To resume, starting from Assemble2 1.2, you will be able to use all the options available from the mfold web server to predict and manipulate your favorite molecule without leaving Assemble2. As you can imagine, more will come, based on the same principle.
In Assemble2 1.2, you will be able to send me any data which may result in an error. The messaging system will warn you that you can report a bug. The data will be automatically included in the content of the message.
Thanks to JavaFX, the upcoming release of Assemble2 will provide you the way to load data directly from several RNA databases (i have started with the Nucleic Acid Database and RNACentral). You will be able to browse the website as you were used to it. Once on a webpage describing a 3D structure (for the Nucleic Acid Database) or a sequence (for RNACentral), a button will be activated, indicating the ability to import the data into Assemble2.
For several tasks (2D prediction, 3D annotation,…), Assemble2 delegates the work to a bunch of Web services. By default, Assemble2 is configured to use our public server (http://arn-ibmc.in2p3.fr/api/). But if you want to speed up Assemble2, you can deploy your own server locally. I have recently updated the way to do it. You will need to install on your machine:
The next releases of Assemble2 will provide a file named “Vagrantfile” containing all the details to transparently install a linux virtual machine containing the webservices needed by Assemble2. For now, you need to download the file from here and to install it in your Assemble2 directory. Once done, go into the Assemble2 directory and type from a command line:
The first time, this will take a while since Vagrant will download the linux virtual machine on your own computer. Once done, type:
This will log you into the virtual machine. Then type from the command line of the virtual machine:
This launches the server hosting the web services. Now start Assemble2, open the configuration panel (File -> Configure -> Assemble2) and change the Web Services Address like the following :
You can download it from this page. The new features and modifications are the following:
- new color themes based on ColorBrewer,
- a multiple selection from the secondary structure navigator can be colored at one go,
- residues selected in the 2D panel keep their original color,
- in the 2D toolbar, the eye icon allows to hide/display absolute positions,
- the secondary structure can be centered on the selection,
- if a recent file is not anymore available, it is automatically removed from the menu “Load Recent…”,
- the algorithm inferring a new 2D and 3D from a structural alignment has been fixed. The 2D structure is inferred first, then the tertiary interactions are added if their residues are conserved between the reference and target sequences,
- Assemble2 can be configured to not launch Chimera at startup and to not pop up the lateral panels automatically,
- two new icons have been added in the 2D toolbar: (i) one to clip the 2D to the upper-left corner of the canvas and (ii) one to make a screenshot of the 2D as a PNG file.