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.