Secondary structure prediction of proteins in Jalview
Channel: Jalview & Dundee Resource Online Training
Date: 2020-04-01

In this tutorial, we explain how to perform secondary structure prediction of proteins using 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/).

The prediction is performed using the Jpred server at the University of Dundee http://www.compbio.dundee.ac.uk/jpred/. For more information, we recommend reading their JPRED-4 research paper (https://academic.oup.com/nar/article/43/W1/W389/2467870/JPred4-a-protein-secondary-structure-prediction).

For this demonstration, I use a group of sequences that have already been aligned, the URL is http://www.jalview.org/tutorial/alignment.fa.

JPred is run by going to the ‘Web Services’ drop-down menu and selecting  ‘Secondary Structure Prediction’ and then ‘JPred Secondary Structure Prediction’. There are two ways that the JPred prediction can be executed, JPred can make predictions from a single sequence or from a pre-aligned set of sequences.  When predicting from a single sequence, JPred first uses PSIBLAST to search the UniProt database and build a multiple alignment.   Predictions made after a PSIBLAST search are usually more accurate but take longer to calculate.

JPred generates a number of sequence-associated alignment annotations. The consensus JPred prediction is displayed in the row called JNetPRED. The helices are represented as red tubes, and the strands are represented as green arrows. The confidence estimates for this prediction is displayed in the JNetCONF row. Higher values mean higher confidence in the accuracy of the prediction.

The consensus JPred prediction is generated from several outputs, such as the HMM and the PSSM profile based predictions. Their results are shown on the JNetHMM and JNETPSSM annotation rows respectively. The JNETJURY annotation row marks where all the profile prediction outputs disagree. Lupas_21, Lupas_14, and Lupas_28 annotations rows predict the presence of coiled-coils. The JNet burial annotation predicts solvent accessibility levels.

The JPRED secondary structure prediction can be performed on a subsection in an alignment if is selection is aligned. JPRED uses this selection as the profile to perform the secondary structure prediction. The first sequence in the set will be used for a JPred prediction.

If columns or part of the alignment is hidden, they will be excluded from the alignment that is sent to the JPred service. The prediction results returned from the service will be mapped back onto the visible parts of the sequence, to ensure a single frame of reference is maintained.

The JPred  prediction can be used to colour the alignment by going to the ‘Colour’ menu, select colour ‘By annotation’ and the select the annotation required. If a 3D structure is known for one protein in the alignment, the JPred prediction can be used to colour the 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).

Video production by Dr Suzanne Duce, School of Life Sciences, University of Dundee.