Protein disorder predictors in Jalview
Channel: Jalview & Dundee Resource Online Training
Date: 2020-04-01

In this tutorial, we explain how to run protein disorder predictions in Jalview. Jalview is a free-to-use sequence alignment and analysis visualisation software linking genomic variants in DNA, protein alignments and 3D structure (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_help/index.html#!Documents/disorderjronn.htm.

The interleukin7 alignment URL used in this video is http://www.jalview.org/tutorial/interleukin7.fa.

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.

This exercise can be found in our User Manual, available to download from the Jalview website (http://www.jalview.org/about/documentation). Other Jalview training videos can be viewed in the training section of the website (http://www.jalview.org/training/Training-Videos).

Jalview can access a wide range of databases including PFAM, PDB, EMBL and UniProt. It can read a variety of file formats including FASTA, PFAM, MSF, Clustal, BLC, PIR, Stockholm.
Jalview collaborates with several groups to offer a broad range of sequence analysis tools including: 
• multiple sequence alignment using Clustal Omega, Muscle, MAFFT, ProbCons, T-COFFEES, ClustalW, MSA Prob and GLProb
• tree calculations and principal component analysis (PCA)
• consensus, conservation, and functional site analysis
• secondary structure and disorder predictions
• visualisation of 3D structure.

Jalview (http://www.jalview.org/) has been developed in Geoff Barton's group (https://www.compbio.dundee.ac.uk/) in the School of Life Sciences (https://www.lifesci.dundee.ac.uk/) at the University of Dundee with the funding support of the BBSRC and the Wellcome Trust. The team has also developed software JPRED (http://www.compbio.dundee.ac.uk/www-jpred) and JABAWS (http://www.compbio.dundee.ac.uk/jabaws).

This video was produced by Dr Suzanne Duce, School of Life Sciences, University of Dundee.