In this tutorial, we explain how to run protein disorder predictions in Jalview. Jalview is a free protein, RNA and DNA sequence visualisation software (
http://www.jalview.org).
There are a variety of protein disorder prediction services available in Jalview. They generate both sequence features and sequence associated alignment annotation rows.
DisEMBL is a set of machine-learning based predictors trained to recognize disorder-related annotations that are associated with PDB structures http://dis.embl.de/. GLOBPLOT predicts natively unstructured regions and regions of globularity. http://globplot.embl.de/. IUPred employs an empirical model to predict regions that lack well-defined 3D-structure under native conditions http://iupred.enzim.hu/. JRONN predicts the region of disorder in sequences based on their local similarity with a gold-standard set of disordered protein sequences
https://www.dnastar.com/protean3d_hel....
For this demonstration, I load the interleukin7 alignment, its URL is http://www.jalview.org/tutorial/inter....
The protein disorder predictors are accessed from the ‘Web Service’ drop-down menu in the alignment window, by selecting the predictor as appropriate from the ‘Protein Disorder’ submenu. On completion, prediction annotation rows appear in the annotation panel below the alignment.
The protein disorder predictors also generate features, these can be displayed on the alignment if in the view menu, the ‘show sequence features’ option is ON. The new features are listed in the Sequence Feature settings dialogue box. The features at the top of the list, will lie on top and thus hide features that lie below them in the list. So it may be desirable to swop their ordering. These features can be mapped onto the 3D structure.
For more information, please look at the ‘Help’ drop-down menu in desktop window or view our User Manual available at http://www.jalview.org/about/document....
Jalview collaborates with several groups to offer a broad range of sequence analysis tools including: (i) multiple sequence alignment (MSA), (ii) tree calculations and principal component analysis (PCA); (iii) consensus, conservation, and functional site analysis; (iv) secondary structure and disorder predictions; (v) visualisation of 3D structure.
Jalview was developed in Geoff Barton's group ( http://www.compbio.dundee.ac.uk) in School of Life Sciences ( http://www.lifesci.dundee.ac.uk ) at the University of Dundee ( http://www.dundee.ac.uk). The team has also developed software JPRED ( http://www.compbio.dundee.ac.uk/www-j...) and JABAWS ( http://www.compbio.dundee.ac.uk/jabaws).
Video production by Dr Suzanne Duce, School of Life Sciences, University of Dundee.
Protein disorder predictors in Jalview computational biology journal | |
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