Colouring protein residues in an alignment using Jalview
Channel: Jalview & Dundee Resource Online Training
Date: 2019-11-07

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/). This video explains how to colour sequence residues and alignments. How to customise colour schemes and threshold colour schemes based on annotations is also demonstrated. Jalview has a number of different colouring schemes available, they are either static or dynamic. The dynamic methods use data such as conservation and consensus to control shading.

The PFAM seed database id used in the video is PF03460.
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.

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