Phosphorylation of bacterial proteins

Jalview Discussion
1

Greetings everyone!

I am relatively new to Jalview so maybe this will seem like a noob question. I am trying to perform a phosphorylation site prediction of the bacterial proteins that I aligned in Jalview. In the demo project, I saw it was possible to do that but I haven’t been able to backtrack and do this for my alignment.

Can anyone provide some insight on this matter?

Thank you all in advance.

Regards,

Nebojsa Bogdanovic

2

Hi Nebosja - thanks for posting your excellent question !

I am trying to perform a phosphorylation site prediction of the bacterial proteins that I aligned in Jalview. In the demo project, I saw it was possible to do that but I haven’t been able to backtrack and do this for my alignment.

You’re quite correct - there is a phosphorylation prediction in the demo project. If you right-click on those sequence features (in the alignment view called ‘Phosphorylation site predictions’) you can open the predictor’s page via the ‘Link’ submenu - which shows URLs associated with features on the sequences in the alignment. Unfortunately, the link no longer works, since the system that Jalview used to display phosphosite predictions was via the now unsupported ‘DAS’ server protocol (see biodas.open-bio.org if you are interested), but you can see from the URL that these predictions came from ''NetPhos-2.0".

Can anyone provide some insight on this matter?

If you wan’t a quick prediction, I’d suggest using
http://www.cbs.dtu.dk/services/NetPhosBac/

It’s really fiddly to get the results back in to Jalview right now - here are some instructions:

  1. Open your Jalview preferences (Tools->Preferences) and in the ‘Output’ tab untick the ‘Fasta’ option in the ‘Append /start-end’ settings. Hit OK to save you preferences.

  2. Now, use Edit->Remove Gaps to temporarily remove all the gaps from the sequences you want to run a prediction on.

  3. Export your sequences from Jalview as FASTA to a text box or file and paste or load them into the form.

  4. Remember to press CTRL/CMD-Z to put the gaps back after you exported !

  5. After loading/pasting the sequences to http://www.cbs.dtu.dk/services/NetPhosBac/ - make sure the ‘Output in GFF’ box is ticked, then hit the submit button and once the prediction is done, copy and paste the GFF file of of the results (starts with ##gff-version 2 and ends with the last line that includes the ID for one of the sequences you input) into a text editor.

  6. The tricky bit - PhosBac doesn’t produce properly formatted GFF2 so you need to do a search and replace for all the lines after the ‘#’ comments, to transform each run of one or more spaces to a single tab character. If you have access to perl on the command line this will work :
    perl -ne ‘(($=~/#.+/) and (print $)) or ($=~s/ +/\t/g and print $)’ < gff2_from_webpage > phoshpobac.gff

  7. You can then drag-and-drop the phosphobac.gff file onto the alignment, or load it on via File->Load Features/Annotations.

Take a look at the built in help or http://www.jalview.org/help/html/features/seqfeatures.html to learn more about sequence features, and of course, there’s also a video (https://vimeo.com/267974633).

Let us know how you get on… hopefully this’ll be a little easier in a future version of Jalview* !
Jim.

  • but someone might write a script to do this before then :wink:
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On 15/10/2018 16:52, #BOGDANOVIC NEBOJSA# wrote:

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Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | [www.jalview.org](http://www.jalview.org) | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)