Hey guys!
I did a multiple sequence alignment with sequences from proteins with disordered regions (IDR). My goal is to see if there is conservation between the 20 proteins for the disordered regions. I already have all the information concerning those IDR since I did the disorder prediction myself. My problem is that I would like to highlight the specific amino acids that are disordered in Jalview using the data that I already have. I do not want to select the regions manually so I was wondering if there is a way to import annotations using my data.
I looked in the manual and I found the basics of it all but I could not find anything that would let me do this automatically, not with the cursor.
I hope this explains my problem clearly and I'll try to find a solution as soon as I can. If someone has an easy answer that would be awesome! :)
Have a good day!
It took some time but now I'm able to create groups from the annotation file, which will help me show what regions are disordered by highlighting them.
Thanks a lot! :)
I just saw that I can't just use annotations like this. By using annotation files it will colour what positions I ask but it's the same thing as doing it manually because amino acids change positions after the alignment. I don't know how but what I really need is to mark certain amino acids, not just position 3 to 15 because when the alignment is done, the "-" characters appear.
I don't know if this makes any sense, I hope someone can help me about this!
Groups are not the way to do this - since they are annotation for alignment columns, rather than sequence positions. In the example above, the
SEQUENCE_REFline tells jalview to add a row of scores - theLINE_GRAPH- to the positions on a sequence, so when it gets realigned, the scores move with the amino acids.If you simply have a list of regions for each sequence that you consider intrinsically disordered, then it sounds like what you need to do is create a GFF file and load it onto the alignment as sequence features. Try this:
First load this sequence into Jalview:
Then save the following line as a text file (it should be a tab delimited file, like you'd save from excel).
You can then load that onto the sequence via the 'Load Features/Annotation' menu. Full documentation is at http://www.jalview.org/help/html/features/seqfeatures.html
Excellent solution! Thank you that is exactly what I need to do!
Now, would it be possible to change the colour of those residues depending on their score? I would like to show the difference in their disorder scores each of them got from the disorder prediction tool I used (score from 0.0 to 1.0, above 0.5 being considered disordered). With what I can do now using your solution, I can only show it in a binary form, which is not very good for global interpretation.
As always thanks a lot for your help you're a life saver! I'm searching for a solution myself in the documentation but if you have a simple answer (that I can't see because I'm not used to Jalview yet), let me know! :)
Have a nice day!
EDIT: Never mind, I found how to do it myself!
Glad the documentation helped :) You can threshold by score, and also apply a linear RGB shade scale with the Graduated Feature Colours option!